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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
Tried this recipe?Mention @perchancetocook or tag #perchancetocook!
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30 Comments

  1. I SO want to try these, but I am allergic to egg. Has anyone tried making these with flax eggs? I’ve read that sometimes that sub works in baking, and sometimes it doesn’t. Thank you!