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Morning Routine Ideas to Cleanse Your Gut

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I’m a huge fan of establishing a morning routine, but for more reasons than to simply have a “good” day. Your morning routine has the power to affect your health in more than one way and your gut health is at the top of the list! Here are some great morning routine ideas to cleanse your gut.

Functional medicine dietitian practicing gut healthy morning routine

Reading Time: 17 minutes

We all need some morning routine ideas, right? Especially if you’re working on healing and cleansing your gut!

For as long as I can remember, my morning routine (or lack of one) has greatly impacted the rest of my day. If you’ve ever slept through an alarm, you know just what I’m talking about. You’ve experienced, firsthand, the negative effects of starting your day in panic, frustration, and hurry. The remainder of your day is likely to feel “off”, at best, and frazzled and unprepared, at worst. Alternatively, when you gently wake up, with time to complete your morning routine, you’re more likely to feel energized, prepared, and focused for the day ahead. 


Undoubtedly, I’m a huge fan of establishing a morning routine, but for more reasons than to simply have a “good” day. A morning routine plays an impactful role in your mental and physical well-being, including:

  • Sets the Tone- How you spend your morning, whether rushed and stressed or relaxed and prepared, has the power to set the tone for the rest of your day. 
  • Increases Productivity- A healthy morning routine helps ensure you are prepared and focused for the day. As a result, I’m willing to bet you’ll check more off your to-do list! 
  • Boosts Mood- Without a doubt, a morning routine elevates your mood and decreases the risk of stress, sadness, and anxiety throughout the day. 
  • Supports Health- Not only can a morning routine reduce stress that can support your mental health, but also physical health. Of utmost importance is gut health because, as we know, every aspect of health starts in the gut. Stress reduction is so important for a healthy gut!

While your morning routine has the power to affect your health in more than one way, your gut health is at the top of the list! Establishing a healthy morning routine can improve your gut by properly prepping the digestive system, increasing gut good bacteria, promoting regular bowel movements, increasing metabolic function, and more! 


Truthfully, how you spend your morning can make or break more than the rest of your day. It can make or break your health, too. Whether you’re heading off to work or school, establishing a healthy morning routine is imperative. That’s why I’m sharing my own morning routine ideas with you!

Personally, I start my day by prioritizing gut health. While I’m nowhere near perfect with this routine and have some days that change, I try my best to protect and guard this time. I encourage my clients to do the same and think about a routine that works for them and their lifestyle. I hope sharing my routine with you encourages and inspires you to start a morning routine of your own, or even add a few morning routine ideas to your personal list if you already have one. 

Morning routine ideas and how your morning routine affects gut health

Before getting into my morning routine ideas, it’s probably helpful to cover a bit of my nighttime routine that sets the tone for the next day. I have an entire article coming soon on this part specifically, but here is just the last part of my routine that sets the tone for my morning routine. 

Since sleep is so important for our health and microbiome, I recommend getting at least 8 hours each night. Lately, I’ve been using a new device called Hatch to help me regulate my circadian rhythm and sleep cycles. What I love about it is that you create and build your own sleep routine from scratch. For my settings, I first created a 30 minute reading light with a beautiful amber glow to start winding down. Regardless of what I’m doing during that time, this instantly calms me. It reminds me of the same glow of the salt lamp I use at my desk during the day.

The next part of the routine transitions to a quick 15 minute mindful meditation with nature sounds. It is an instant stress relief and really sets the tone for relaxation. The Hatch then transitions to a 20 minute white noise. It is seriously so calming and gives me the feeling of sitting on a beach at sunset. My husband and I usually like to pray during this time for our family, thank God for the day, bring any requests to Him, and ask for protection while we sleep. At this point, the regular white noise eventually starts without any light at all. I use a very simple plain setting that puts me right to sleep. 


What I love about using the Hatch is that I have a setting where the light starts to gradually increase each hour and mimic a sunrise. It actually starts “rising” around 5:30am even though we don’t have to wake up until 7:00am. What’s so great about using this as an alarm clock is that it actually isn’t an alarm clock at all. I don’t know about you but I always hated and fought with my alarm clock growing up. I would snooze it multiple times and the noise would startled me and wake me up in a panic.

Those days are long gone. Since using the Hatch, we don’t need an alarm clock because the light eventually wakes us up naturally around 6:30-7:00. I have noticed feeling so refreshed and rejuvenated using this method to start my morning routine. If for some reason I don’t naturally wake, my Hatch starts morning nature noises, such as birds chirping. This is the perfect way to wake up calmly. 

I will admit I (sometimes) have a bad habit of checking my phone once I wake up. It’s really tempting to check emails and social media first thing in the morning. I know how damaging this is and how it isn’t the best way to begin the day, and try to make a conscious effort to get up before that. That is one of my personal goals as of lately and something I am committing to and conscious of. 


You can’t start anything until you clean your mouth and brush your teeth. I take oral health seriously because the mouth is a part of your gut microbiome and home to your oral microbiome. It’s directly correlated with our gut health and health in general. Poor oral health is even linked to inflammation, inflammatory bowel disease, brain fog, aging, autoimmune conditions like diabetes, and even obesity. 

Microbes, enzymes, and nutrients pass through your mouth making their way to your gut. In fact, your mouth has a microbiome of it’s own. This is why your mouth and gut microbes are constantly interacting with one another. Digestive problems can directly affect your oral health and vice versa. If your digestive health is good, it’s likely you’ll feel good. This is because your gut microbiome is in control of many processes in your body. 

I use a non-toxic and all natural RiseWell toothpaste (the absolute best) to brush. I use their mouthwash to rinse too. If I’m showering in the morning, I actually oil pull at the same time using organic extra virgin coconut oil. Oil pulling has been part of my routine for a while and I love it. At first, it took me awhile to get the hang of and felt like such a long process. Now I multitask while pulling to keep it simple. 

Oil pulling benefits the body by removing toxins, killing bacteria, and reducing inflammation in the mouth, and therefore, the rest of the body (including the gut). I recommend using coconut oil for oil pulling and following the simple instructions below. Additionally, you can use a tongue scraper to further rid the body of pathogenic toxins. I always finish my teeth routine with a quick tongue scraper to remove any remaining bad bacteria that builds up overnight. 

Morning routine ideas like practicing good oral hygiene
How to Start Oil Pulling
  1. Place a tablespoon of coconut oil in the mouth. You can also try olive oil or sesame oil if you don’t like the taste of coconut oil.
  2. Sit upright and swish the coconut oil around the mouth for 15–20 minutes or while doing basic household tasks. If you have a difficult time keeping the coconut oil in your mouth for this length of time, you can start with 5 or 10 minutes and slowly increase the duration. 
  3. It is essential to keep swishing and to breathe through the nose. Do not swallow the oil. Once done, spit the oil in the garbage (not the drain). Avoid spitting into the sink or toilet, as it can lead to clogging. Do not swallow the coconut oil when finished. 
  4. Wait 20 minutes to brush your teeth again to allow the retention of good bacteria and the rebalancing of the oral microbiome. I also recommend using a separate toothbrush after oil pulling to the one used for daily teeth cleaning. 
  5. Aim to oil pull a few days a week! 

I know this might sound silly, but making my bed is actually huge for me! If I don’t make my bed in the morning, I feel as though I don’t have a great day. Making my bed helps me feel organized and less scattered. It is also the first thing I accomplish that day that is moving things forward. This starts to shift my mental health and makes me more motivated and productive throughout the day. There’s also several studies on this too! 

If you haven’t seen the speech by the Navy seal who talked to a graduating class about how to be successful in life, you have to watch the 6 minute highlight version of it here! He actually shares why people who make their bed each morning are more successful in the beginning. Making your bed in the morning can change your life and even the world! 

The entire 20 minute speech is here if you’re interested. It might make you cry, and if not, it will motivate you in an incredible way!


This is a given and nothing special but one thing I try to do is have something ready and picked out the night before. I typically only do this when I’m going to be on video and with clients. I like the fact that I don’t have to think about what to wear because that takes up brain energy. We have to make so many decisions in our day and studies show how that can create stress and fatigue. Choosing what to wear the night before allows you to make one less decision during the hours where your brain is sharp. I like to reserve that as much as possible!

 If it is going to be a full day of behind the scenes work, I usually dress comfortably. Adjusting to seeing clients online after seeing them in person was tough for me at first. I found I had to force myself to do makeup, dress up, and pretend I was going to an office to be productive. After 3 years of helping clients online, I’m able to show up productive dressed up or more casual. 

I do find that I perform my best though when I put effort into getting ready the same way I would if I was out and about. I try to take a few extra minutes to do my hair, some light natural makeup, and choose a comfortable, yet professional outfit. 


I’m that kind of person who wakes up really hungry! It never used to be this way until I started really making an effort to regulate my meal timing throughout the day. My natural internal clock tells me when it’s time to eat. I typically head downstairs for breakfast around 7:30-8:00am. 

The first thing you eat or drink has the ability to set the whole tone for the rest of the day. So before I eat anything or make a fresh cup of coffee, I hydrate! This is so important because our body naturally detoxes while we sleep. We must hydrate well first thing in the morning to remove those toxins. In addition, I add fresh lemon or apple cider vinegar to my water in the morning to alkalize my pH. This activates stomach acid which helps to breakdown the food you eat throughout the entire day. 

Start by squeezing half of a lemon or add 2 tsp of apple cider vinegar to 12oz of warm water and sip slowly. This not only improves stomach acid, activates gastric juices and enzymes, but it also stimulates the bowels for proper toxin elimination. I also find it really nice to enjoy something warm to gradually prepare for my next meal, a cold smoothie! Instead of shocking the digestive system with something cold right away, I am easing into the day by gradually waking everything up and preparing my body to work and process everything in a gentle way. 


Probiotics are key for a healthy microbiome and help to repopulate good gut bacteria. I personally test my gut bacteria once a year so I can personalize the probiotic that is right for me. This is the same method I teach clients because sometimes the wrong probiotics can do more harm and cause more GI distress. This is why it is so important to test, not guess and find the strains your body is lacking and needs the most. While diet can provide many natural probiotics, I find some individuals, especially those with autoimmune conditions, benefit from taking additional supplemental probiotics in addition to dietary probiotics. 

I take a probiotic with specific strains my gut needs to thrive with my breakfast. Most probiotics are best taken before food on an empty stomach to limit exposure to digestive enzymes and bile salts. This won’t apply to everyone and some strains are best with food or after dinner. It all depends on you and your unique chemistry. For me, I take mine right after I hydrate so there’s some time in between before my actual meal. 

If you’re not sure what your gut bacteria looks like and haven’t tested your gut, I highly recommend Seed probiotics! It’s a 24-strain broad spectrum prebiotic and probiotic that is very well made to sustain stomach acid and bile acids to ensure proper delivery to the colon. The strains are well studied for the majority of the population if you aren’t able to customize a probiotic to fit your unique needs. Most people do very well on this particular probiotic and experience great results. I often put my clients on Seed once they’ve healed their gut and we are in maintenance mode. 

You can check out Seed probiotics, here.

Taking a probiotic is a good morning routine idea

Sometimes I like to take a break from probiotics for a few months and switch to a few spoonfuls of Coconut Cult yogurt. You can sometimes find this at your local health food store or use their website to locate a place that carries it by you. Not only is this yogurt dairy free and delicious, but it contains 25 billion probiotics that are highly active. You only have to eat 2 quick spoonfuls to get this amount, which makes it a really fun way to get probiotics in. I find it can be a challenge to limit myself to 2 spoonfuls when they have flavors like vanilla toffee (tastes like icing), chocolate mousse, and mango cream. You really do want to ration it though because too much of it at once might cause a stomach ache if you aren’t used to all those strains. 


Next on the agenda is my morning smoothie. I never get sick of these because I always alternate the varieties and flavors. Smoothies have been essential to my digestion and energy over the years! Having a pre-digested meal that is easier to break down, such as a smoothie, is similar to the warm water in the same way that it  prepares your digestive tract to slowly “wake up”. Not only is it extremely nourishing and healing for cells to drink a smoothie in the morning, but it helps the gut achieve digestive rest for easy nutrient transport.

I suggest a balanced smoothie with the right amount of protein, healthy fats, carbs, and fiber, to keep you full and satisfied. When I make my smoothies, I go down the list to make sure I am getting everything I need to make it a complete meal. This is usually so filling that I am satisfied until lunchtime. If you are new to smoothies, below is one of my absolute favorites and go to recipes!  

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Blueberry Pie Smoothie

  • Author: Nikki Yelton
  • Total Time: 5 minutes
  • Yield: 1 serving 1x


This blueberry pie smoothie is not only delicious, but balanced with the right amount of protein, healthy fats, carbs, and fiber, to keep you full and satisfied. 


  • 1 cup filtered water
  • 1 tsp beetroot powder
  • ½ tsp cinnamon powder
  • 1 cup frozen or fresh blueberries 
  • ½ frozen banana 
  • 1 serving Nuzest Clean Lean protein powder
  • 1 tbsp ground flaxseed
  • 1 tbsp almond butter
  • 1 cup frozen zucchini slices 
  • 23 ice cubes (optional) based on desired thickness 


  1. Place all ingredients in your blender and blend until smooth. Pour into a glass or smoothie container and enjoy! 


Optional Toppings: Grain free granola, coconut chips, chocolate chips, or bee pollen 

Nut Milk: You can use organic unsweetened nut milk in place of filtered water

No Blueberries: Use any type of frozen berry instead

No Nuts: Sub sunflower seed butter instead

  • Cook Time: 5 min
  • Category: AIP, Gluten Free, Dairy Free


  • Serving Size: 1
  • Calories: 223
  • Fat: 12g
  • Carbohydrates: 26g
  • Fiber: 9g
  • Protein: 6g

Keywords: gut healthy smoothie, morning smoothie, healthy smoothie, blueberry smoothie


After I’ve had my water and smoothie, I’ll pour myself a warm cup of coffee and head up to my office to begin the work day. I take my coffee very seriously and I am a bit of a coffee snob. Fun fact: my family and I owned and ran a coffee shop for over a decade. That experience definitely contributed to my coffee obsession. One cup of quality coffee in the morning is enough to satisfy me and keep me going throughout the day. I actually alternate between regular and Swiss water decaf so I’m not dependent on caffeine. This gives me more energy and I feel clear when my body isn’t addicted to caffeine. I enjoy coffee more for the taste and comfort, and I don’t rely on it for the short-term energy boost it is known for. 

For years I’ve been using Purity coffee and it is the ONLY brand of coffee I’ll ever use. Once you try purity you will never be able to go a day without it. Not only is it delicious but it is the only coffee I trust that is truly “beyond organic”. Since most coffee (including organic) is loaded with toxic substances, molds, and mycotoxins, it can eventually wreak havoc on the gut.

I used to encourage my clients to remove all coffee from their plan while we work on healing the gut. But then I discovered Purity Coffee. Since the quality is so good and free of the things that can aggravate the gut lining, I’ve been able to keep it into my clients routine! They are so happy about the fact they can enjoy coffee still WHILE healing the gut. You can check Purity out here and use the code NYELTONRD5 at checkout for a discount. 

For the rest of my coffee routine and for tips on how to brew a safe cup of coffee without the PBA’s and harmful plastics in machines, check out my resource page and scroll to the section called “The Best Cup of Coffee”. I usually add a scoop of collagen peptides and use a small amount of original Nutpods non-dairy creamer. You can read more about the gut health benefits of collagen here, and this post about my 4 favorite non-dairy coffee beverages to add to your morning routine ideas, here


At this point of the day I’ll bring my coffee up to my office and settle in to where I’m going to be for the next 8+ hours. Since I work from home, I like to make sure my environment sparks joy and is a place of productivity. Since I don’t do well with clutter, I’ll make sure my work station is neat. I also like to open the blinds and get natural light in for vitamin D exposure. This really energizes me throughout the day. If it’s a nice day, I’ll open the window to get some fresh air in and hear the sounds of nature. This always helps my productivity (except on Tuesdays when the weed wackers come around). 

During all this, I add water to my office diffuser and usually add a few drops of brain power essential oil blend by Young Living. I personally love Young Living’s quality oils and blends and will always switch these up based on what I have going on. I use brain power the most while working because it truly helps me get in the zone and energizes my mind. This scent makes me feel clear and ready to tackle the day. I also have a diffuser that has gentle and soft music playing in the background. It is extremely calming and peaceful! 

If you are new to oils, I highly recommend a starter kit that contains the key oils for a healthy lifestyle. It also includes a diffuser, too! You can enroll as a new member here and join my oil team if you are ready to start using them more for your home and health. 

Since I usually need to start work right away, I’ll read a short daily devotional and spend a few minutes praying for the day ahead. There’s so many great devotionals I’ve used over the years, and lately I’ve been using the First5 app for a verse to meditate on. If I’m working with clients, I like to pray for their health and healing and that God will give me the strength and wisdom to help them that day. I usually spend more structured time in prayer later in the day or when I go for my walk so this is a quick way to center myself before beginning work. I find when I skip this, I am scattered, overwhelmed, stressed, and not myself. Taking this pause while I sip my coffee is a special time I cherish! 


I’m super productive in the morning and this is when I do my best creative work. Instead of simple tasks or housework, I always get right to work. I try to block out the first hour or two of my work day for specific tasks that take the most mental power. Simple tasks are saved for later in the day when my energy naturally starts to decline towards the end of the workday.

I personally use Trello to organize my entire life, literally! I use it for my business workflows, team workflows, chore and grocery list workflows, etc. It helps me organize my life in so many ways and reduces stress because I’m able to keep track of everything. If things stay in my head all day, I get overwhelmed and stressed easily. I love how simple Trello is to keep my thoughts, tasks, and to do lists in one place. I’ll always organize my trello board for the next day once I wrap up a work day. This way when I log in and start work after my morning routine, I see the whole day in front of me and can budget my time efficiently. 

At this point, my morning routine is complete and I’m diving into the work day. I feel great after all this and I’m in the zone, ready to take on the day. It’s usually 8:15-8:30 when I get to this point and begin working. Sometimes my husband and I will take turns making the coffee and smoothies for each other. That is a real treat because it gives me more time to spend on the routine I detailed above. I’m usually able to begin work earlier on those days too and get ahead!


There are many things you can do for an effective morning routine. What I shared is what works for me and my schedule. There’s also so many beneficial practices I wish I had more time for and could incorporate daily. There are so many gut healthy morning routine ideas out there! Here’s a list of some other suggestions to enhance yours.

Incorporating gratitude

I love using my gratitude journal to jot down 3+ things I’m grateful for. Gratitude has been scientifically-proven to increase joy and peace, which I’ve witnessed, firsthand.

Getting outside in nature

Getting fresh air and sun in the morning is incredibly healing and energizing. This might look like sitting on a porch or taking the dog for a walk. Added bonus if you can walk around for a few minutes barefoot. The soil is naturally grounding and healing. 


Some people love it and some can’t even think about working out until later in the day. I’m one of those people who can’t get myself to do activity in the morning. This is probably because I’m so productive with work early in the day and I don’t want to waste that. If exercise energizes you and helps set the tone for the day, this can be a great addition to a morning routine! 

Yoga or stretching 

Yoga and or stretching helps improve circulation and blood flow. It is also an excellent way to set the tone and enter the day feeling calm, relaxed, and grounded. 


Whether it be a good book, devotional, magazine, or newspaper–many people enjoy incorporating reading into their morning routine. 

Prayer & Worship 

Spending a structured time in prayer in the morning is a beautiful way to spend time. As a Christian and follower of Jesus, this is something I love doing on weekends because I’m not thinking about work. I can spend more quality time praising God, praying for others, bringing any personal requests to Him, and meditating to worship music. 


Sitting in silence and letting your mind wander can be restorative, calming, and peaceful. You can do this anywhere for 7-10 minutes and practice being still. It’s a great way to ease into the day! 

Set goals or intentions

Write out goals for the day or week and some intentions you have. When we write things down, it becomes more real and we are more eager to accomplish them. 

Listen to music or dance

Why not start your day in a cheerful way and get your blood moving a bit. Sometimes you just have to sing or dance it out. I used to do this when I would commute over an hour to work back in the day. It made the trip fun and energized me. 

Listen to a TED talk or podcast 

Getting educated on a topic or hobby that interests you can spark creativity throughout the day. There’s endless amounts of talks and podcasts on just about every subject out there! 

Meal Prep

If you’re someone with a busy lifestyle or schedule, this can be a great time to ensure you have nourishing meals packed and ready to go. 

Write a to do list 

If you’re the type of person who likes to plan your days out, writing out a personal agenda or to do list might be a helpful way to start your day. 

Social media

If social media brings you joy, spend 5-10 minutes catching up on something you enjoy or connect with others. 

Water the plants

A few minutes in the morning might be a great time to water your plants or garden. Not only are plants healing to the body, but they are also calming to look at. 

Do a crossword puzzle

Crossword puzzles can stimulate and sharpen the brain in less than 20 minutes. This can be a nice way to also ease into the day and activate your brain. 

Taking care of littles

Sometimes a morning routine looks like taking care  of little ones. If this is the season you’re in, see how you can incorporate this into your own routine too and make it fun! Chances are your children will get used to the routine and grow to appreciate it. We all thrive on routine, regardless of age! 


If you’re new to the morning routine game, here are a few, easy steps and morning routine ideas to get you started!

  • Choose 1-2 action steps from my own morning routine ideas or from the list of other suggestions listed above. Implementing too many steps at once can be easily overwhelming. Start slow and implement 1-2 steps at a time. 
  • Commit to those action steps every morning. Consistency is key!
  • Give yourself grace when you slip up. Notice I said “when,” not “if.” We’re all imperfect humans, so learning to extend grace to ourselves is a crucial first step.

Establishing a morning routine is not only beneficial for the mind, but also the body- specifically, your gut health! I’m willing to bet you’ll notice physical and mental improvements within a day or two of consistently sticking to your morning routine. 

How to create a morning routine for gut health

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"When it comes to balancing our body, healing the gut, reversing autoimmunity, and achieving optimal health—we are a lot like a car that won’t run right. In order to fix the problem once and for all instead of relying on jumper cables, we must get underneath the hood, run the diagnostics, and replace the battery so that it runs good as new."

-Nikki Yelton, RD

a note from nikki:

If you are ready to stop wasting precious time, get off the never-ending hamster wheel, and finally surrender trying to figure things out on your own—this is your moment. 

You don’t have to settle for just getting by and hoping tomorrow is a better day. We both know you are a woman who deserves better and are made for so. much. more.

are you ready?

Ready to resolve your GI distress, reverse autoimmunity, and live your extraordinary life?

I believe every woman can take back their health!

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