5 from 3 votes

Gut Healthy Trail Mix Breakfast Cookies

 March 15, 2022

If there’s one health “trend” that I’d like to see in 2022, it’s the idea of cookies being a breakfast food. Especially when they’re this delicious, vibrant, and healthy! My Gut Heathy Trail Mix Breakfast Cookies are the perfect cookie to help you start your day off on the right foot, while ensuring that you’re supporting both your gut health and your overall health, in the process. They are loaded with healthy fats, fiber, and plant-based ingredients, but don’t be hesitant – they still taste like delicious cookies!

A baking sheet lined with parchment paper with six gut healthy trail mix breakfast cookies lined on top. A small bowl of pumpkin seeds and a bowl of cookie dough with a cookie scoop sit to the side.

Friends, when was the last time that you got to eat cookies for breakfast?! For me, if I’m being honest, it was just the other day, when I was rummaging through my pantry in search of ingredients to make a cookie that would fulfill my morning sweet tooth cravings. I grabbed a load of my favorite, healthy ingredients, and whipped these bad boys up. And let me tell you, the impromptu breakfast cookie did NOT disappoint!

In fact, it was so good that I just had to share them with you here. These cookies have a little bit of everything that I love. They’re sweet, they’re slightly salty, they’re nutty, they’re fruity. Should I go on?! Think of these as a healthier twist on a “kitchen sink” cookie, except made with ingredients that are good for your gut! While I love a more conventional cookie recipe, like my Life Changing Tahini Chocolate Chip Cookies, or my Best Ever Chocolate Chunk Olive Oil Cookies, this cookie recipe is perfect for breakfast, and for helping you start your morning off on the right foot!

Plus, I’m excited to partner with my friends at  Seed, the maker of the amazing DS-01™ Daily Synbiotic, to bring you this recipe. Seed’s Daily Synbiotic is a huge part of my daily life, and is the number one product that I rely on for maintaining my optimal gut health!

A wire backing rack with freshly baked gut healthy trails mix breakfast cookies, alongside a jar of Seeds DS-01 Daily Synbiotic supplement.

How I Maintain a Healthy Gut

For me, maintaining a healthy gut comes down to two main things: 1. Making sure that my diet is full of gut healthy ingredients (and, subsequently, is lower in inflammatory ingredients) and 2. That I am also taking the right supplements. And when I say supplements, I really mean making sure that I’m taking a quality probiotic. Because let’s be honest, probiotics = life (literally!)

For the past few years, I’ve been taking the Seed Daily Synbiotic, and it has been a game changer, and that’s because it’s both a probiotic and prebiotic rolled into one. And, not to mention, the capsule is made with two layers, so that the inner probiotic capsule actually makes it to your colon (and eventually the small intestine) intact.

Most probiotics on the market die in your stomach, thanks to our stomach acids and such, rendering them ineffective. And, Seed contains 53.6 Billion AFU, which means it’s powerful AF. Like all things in life, you can’t take a supplement for a day and expect it to work a miracle. Be consistent and commit to supporting your gut health. Trust me – it’s worth it.

If you want to try Seed for yourself, use code KALEJUNKIE15 for 15% off your first month’s supply.

A close-up of three rows of gut healthy trail mix breakfast cookies, all lined up on a baking sheet.

What You Need to Make These Gut-Friendly Cookies

To make these cookies, you need some basic cookie ingredients as well as some special gut healthy ones. What constitutes a gut healthy ingredient, you may ask? To find this out, I consulted with Seed’s Periodic Table of Microbiome Friendly Foods. This periodic table shows the most beneficial ingredients for supporting our gut health. And luckily, some of my favorite ingredients were on the list.

For this recipe, I wanted to highlight a few of these key ingredients:

  • Oats: Did you know that oats are a prebiotic food?! It’s true! They help to feed specific, good bacteria in our gut, and can be thought of as nature’s prebiotic. Plus, they’re also high in soluble fiber, which help keep our guts clear and “regular,” if you know what I mean. 😉
  • Flax Seeds: Flax seeds are full of plant-based protein, fats, and fiber, making them an all-around staple for a gut healthy diet! Plus, they contain “lignans,” which help to mitigate inflammation levels.
  • Pumpkin Seeds: Pumpkin seeds are packed with powerful antioxidants and healthy fats. Yum! They also contain essential minerals like magnesium and zinc, which can help us metabolize our food.
  • Chia Seeds: Chia seeds are high in Omega-3’s, which can lower our blood pressure, help our cardiovascular health, and keep our skin looking clear! Many of the best sources for Omega-3’s lie in fish protein, but chia seeds are a wonderful plant-based option!
  • Applesauce: Apples (and applesauce!) are rich in fiber, antioxidants, and Vitamin C, and also contain pectin, which can help positively impact gut health.
  • Almonds: One of the best foods for lowering our cholesterol levels and increasing Vitamin E, almonds are a staple in my household. Especially in the form of almond milk!

And to make these cookies, you’ll also need the following healthy ingredients as well:

  • Cinnamon: The cinnamon adds the best taste, so don’t skip it!
  • Baking Powder: Baking powder will ensure that these cookies rise, and stay nice and fluffy on the inside!
  • Dried Cranberries: Dried cranberries are high in Vitamin C, and are just absolutely delicious. They truly add the perfect touch of sweetness to this recipe!
  • Vanilla Extract: Would it truly be a cookie recipe without the vanilla extract?!
  • Maple Syrup: I love maple syrup because it adds sweetness to the recipe without the refined sugars, which can be hard on our gut!
  • Coconut Oil: A little coconut oil helps these cookies stay bound together, so you can get that perfect bite, every time.

How to Make These Healthy, Chewy, Seedy Cookies

Making these cookies could not be any easier! Simply start by preheating your oven to 325 F and line a baking sheet with parchment paper.

Next, mix together ALL of your dry ingredients in a bowl, followed by all of the wet ingredients.

Once they’re fully incorporated, let the mixture sit for approximately 10 minutes. This is KEY!

Then, use a cookie scoop to form 8 perfectly round cookies. Line them up on your baking sheet and and gently press down with the palm of your hand to flatten them out, so they don’t spread!

Finally, bake for 15-16 minutes, or until done. Once they’re done, let them cool, and then enjoy!

Ready to Try out Seed? Let’s do This Thing!

If you are interested in trying out Seed, I’ve linked it for you, and you can use code KALEJUNKIE15 at checkout to save 15% off your first month’s supply of Seed’s Daily Synbiotic. I can’t wait to hear how Seed is working for you, so if you decide to try it out, be sure to come back and leave a comment below!

**This post is sponsored by Seed. However, all information and opinions shared in this post are 100% my own. I share only products and services that are a part of my life and that I wholeheartedly love. 
** Photography by Gayle McLeod
Dairy Free/gluten-free/Grain Free/Nut Free/Paleo/Refined Sugar Free/snacks/Vegan

Gut Healthy Trail Mix Breakfast Cookies

5 from 3 votes
Nicole Modic
Prep Time 15 minutes
Cook Time 15 minutes
Total Time 30 minutes
SERVES 8 Cookies
Print It Pin It
If there's one health "trend" that I'd like to see in 2022, it's the idea of cookies being a breakfast food. Especially when they're this delicious, vibrant, and healthy! My Gut Heathy Trail Mix Breakfast Cookies are the perfect cookie to help you start your day off on the right foot, while ensuring that you're supporting both your gut health and your overall health, in the process. They are loaded with healthy fats, fiber, and plant-based ingredients, but don't be hesitant – they still taste like delicious cookies!



  • 1 Cup Rolled Oats
  • ½ Cup Oat Flour
  • 1 Teaspoon Cinnamon
  • ¾ Teaspoon Baking Powder
  • ¼ Cup Ground Flax Seeds
  • 2 Tablespoons Chia Seeds
  • Cup Dried Cranberries
  • ½ Cup Pumpkin Seeds unsalted
  • 2 Teaspoons Vanilla Extract
  • ¼ Cup Maple Syrup
  • ¼ Cup Applesauce
  • 3 Tablespoons Coconut Oil
  • 2 Tablespoons Milk of Choice, plus more if needed I use almond milk, but any type of milk works here!


  • Start by preheating the oven to 325 F.
  • Line a baking sheet with parchment paper and set aside.
  • Next, in a large bowl, mix together all of the dry ingredients (including the seeds), followed by all of the wet ingredients.
  • Stir everything to incorporate well, and let sit for 10 minutes.
  •  If the mixture is too thick, feel free to add in another tablespoon or two of milk.
  • Once the batter has set, use a cookie scoop to form 8 cookies on your baking sheet.
  • Use the palm of your hang to gently press down on the cookies and flatten them. This will ensure that they don't spread too much!
  • If desired, sprinkle some more pumpkin seeds and/or dried cranberries on top of the cookies.
  • Bake for 15-16 minutes.
  • Once done. remove from the oven, let cool, and enjoy!

Did you make this recipe?

I’d love to see what you made – tag @kalejunkie
in your posts and I’ll re-share!



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    • Hi Maxine! This recipe has not been tested that way, but I don’t see why it wouldn’t work! ☻

  1. 5 stars
    I just made these for my work lunches this week and they are delicious! I had a mix of cranberries/sunflower seeds/pumpkin seeds and tossed them in!

    • Yum! That sounds like a delicious addition to these cookies, Danielle! Thank you so much for making them, and for leaving such a kind review!

  2. Wow, these cookies are great. I ate two and I am stuffed! One is good. I ran the ingredients through a nutrition facts finder and found that two of these have roughly 225 calories; 13 grams of fat; 24 grams carbs with ~4 grams of fiber; 6 grams of protein! So cut those numbers in half if you’re just eating one. These would be amazing on a hike to recharge or around a workout. Thanks for the recipe!

  3. I can’t have oats and made these subbing oats for quinoa flakes, and the oat flour for almond flour, and they are so delicious!!!! I am wondering how long these will keep? Thanks!

    • Hi Aura! They should last about one week, when stored in an airtight container in the refrigerator. Thanks so much for making this recipe!

  4. I would love to make these but I am allergic to apple and don’t have bananas, how can I substitute applesauce? thank you ♡

    • Hi Victoria! You could try substituting the applesauce for steamed and mashed sweet potato. However, please note that this recipe has NOT been tested with it, so I cannot guarantee that it will turn out the same. That said, if you do decide to try it, please let me know how it goes!

    • Loraine, I am so sorry to hear that. I am sending you and your son so much healing and loving energy. I hope these cookies helped to lift your spirits a little bit!

    • Hi Linda! You can just omit the coconut all together, or add a touch more of maple syrup to add the sweetness that the coconut would add! 🙂