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These healthy chocolate cherry muffins are fluffy and delicious muffins bursting with baked juicy cherries and chocolate flavors. They are made with healthier ingredients like almond flour, olive oil and coconut sugar.

Healthy chocolate cherry muffin cut in half.

Cherries are one of my favorite fruits. I love to eat them, bake with them, and cook with them as often as possible! If you do too, check out my Chocolate Cherry Smoothie, Almond Flour Chocolate Cherry Lava Cakes, and Gluten-Free Apple Cherry Crisp.

I especially love these healthy chocolate muffins with cherries. They are naturally gluten-free, dairy-free, Paleo, and delicious!

Paleo cherry muffin cut in half.

Why this recipe works

  • Chocolate and cherries are a wonderful combination.
  • This recipe is great for those following a Paleo or Gluten-free diet.
  • This recipe is allergy friendly. It is soy-free, peanut-free, gluten-free and dairy-free.
  • It is a crowd pleaser!

Recipe ingredients

Ingredients needed to make paleo cherry muffins.
  • Almond flour– blanched almond flour works best for baking because it is more refined in texture.
  • Tapioca flour– this type of flour helps give a good texture to Paleo or gluten-free baked goods.
  • Coconut flour– this is very absorbent so don’t use more than the recipe requires.
  • Coconut sugar– this has a lower glycemic index than other sugars.
  • Cocoa powder– make sure to use one that is unsweetened.
  • Baking soda– this makes the muffins rise.
  • Cream of tartar– I like baking with cream of tartar because it results in great texture.
  • Eggs– this help bind the muffins together.
  • Almond milk– make sure there is no added sweetener or flavor.
  • Olive oil– this is used to replace butter in the recipe. Any kind of olive oil works here.
  • Chocolate chips– make sure to use ones that fit your dietary needs. I like HU chocolate chips for Paleo baking.
  • Pitted frozen or fresh cherries– both work. If using frozen, you don’t need to let them thaw first. Just use them straight from the freezer.

See recipe card below for a full list of ingredients and measurements.

Additions/ Substitutions

  • Instead of tapioca flour, you can use arrowroot powder.
  • Instead of coconut sugar, you can use brown sugar, but then the recipe won’t be Paleo anymore.
  • Instead of almond milk, you can use any non-dairy milk of choice.
  • Instead of olive oil, you can use avocado oil.

Step by step instructions

Dry ingredients in a bowl.
Step 1

Step 1: Mix the dry ingredients together in one bowl. This includes the almond flour, tapioca flour, coconut flour, coconut sugar, cocoa powder, baking soda, cream of tartar, and salt

Wet ingredients added to the dry bowl.
Step 2

Step 2: Add the eggs, almond milk, and olive oil, to the dry ingredients and mix. 

Chocolate chips and cherries added.
Step 3

Step 3: Fold the chocolate chips and cherries into the batter.

Chocolate paleo muffins with cherries in a loaf tin.
Step 4

Step 4: Bake!

Healthy chocolate muffins with cherries cooling on drying rack.

Recipe FAQs

Can you use frozen cherries?

Yes! Just throw the frozen cherries into the batter. They don’t need to be thawed.

How do you store these muffins?

I like to keep them covered and then keep them on the counter for up to 3 days.

Can you freeze them?

Yes! Make sure they are fully cooled off first then individually freeze them in freezer friendly bags or containers.

Other Paleo Muffin recipes you’ll love

Did you try this recipe? Please leave me a ⭐ review below!

4.93 from 14 votes

Healthy Chocolate Cherry Muffins (Paleo, Gluten-free)

Servings: 12 muffins
Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes
Paleo Chocolate Cherry Muffins (GF) | Perchance to Cook, www.perchancetocook.com
These gluten-free and Paleo muffins are fluffy, chocolatey and are bursting with warm juicy cherries. Made with almond flour, tapioca flour, and coconut flour.

Ingredients 

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Instructions 

  • Preheat oven to 350 degrees F. Grease a 12 cup cupcake tin or use liners.
  • Combine the almond flour, tapioca flour, coconut flour, coconut sugar, cocoa powder, baking soda, cream of tartar, and salt in large bowl.  Mix with a fork until everything is blended together.
  • Add the eggs, almond milk, and olive oil, and mix well. Stir until well blended. Fold in the chocolate chips and cherries.
  • Evenly spoon the batter into the muffin tins.
  • Bake for 18-20 minutes.

Notes

  • Instead of tapioca flour, you can use arrowroot powder.
  • Instead of coconut sugar, you can use brown sugar, but then the recipe won’t be Paleo anymore.
  • Instead of almond milk, you can use any non-dairy milk of choice.
  • Instead of olive oil, you can use avocado oil.

Nutrition

Serving: 1muffinCalories: 296kcalCarbohydrates: 23.4gProtein: 5.9gFat: 22.8gCholesterol: 31mgSodium: 167mgPotassium: 253mgCalcium: 52mgIron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American
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30 Comments

  1. Incredible! Tasted like an expensive chocolate cake from a fancy restaurant. I just brought home a ton of fresh cherries that we picked on vacation and needed a paleo recipe. This was perfect! Simple to put together and a total reward to eat. I used fresh tart cherries and dark chocolate chips from Trader Joes (72%) Both my husband and I loved it! Make sure to warm up just a little bit if they aren’t fresh from the oven so the chocolate melts as you eat it!5 stars

  2. These are good but the olive oil gives them a slightly off bitter taste (even with my good quality extra virgin olive oil). Next time I think I’d use a more neutral oil like avocado. I also upped the sweetness with a little stevia4 stars

  3. This was superb! I made a little loaf and used date sugar for the additional minerals and ghee. It was so chocolatey goodness. I also used Lily’s dark chocolate chips (sugar free). Thank you for sharing this recipe5 stars

  4. I was looking for a chocolate cherry recipe for a birthday party. I made a test batch and it was a hit with my husband, sons, and friend. Then, I made about 100 for the party. They were a big hit. It’s great to have something healthy that I’m happy to have leftovers of. The one tweak I made is to substitute ghee for olive oil.  I did use frozen cherries and threw them right into the batter.  Thanks so much for the wonderful recipe! 5 stars

  5. I’ve died to try these since seeing the pin. So I did. And I have to say the texture is perfect! Everything is perfect about these muffins except they need a little more sweetener. Next time I’ll add in some more coconut sugar or maple syrup or something. They’re just not sweet enough for me. Great though.

    1. Yay!!! Happy to hear it! I bet the chocolate flavor will taste ever better with a bit more sweetener. 🙂

  6. Chocolate and cherry is my favorite combination! Your photos are gorgeous ! Despite the fact that I just had dinner, I am imagining how great this would taste!

  7. I have to try these! I am always looking for good Paleo recipes as sometimes I like to eat from that lifestyle.

  8. I’m going to have to make these. My husband loves all things cherry and I love all things chocolate, so together it’s the perfect duo!5 stars