These healthy chocolate cherry muffins are fluffy, chocolatey and bursting with juicy baked cherries. They use wholesome ingredients like almond flour, olive oil and coconut sugar.
Cherries are one of my favorite fruits to eat and bake with. If you enjoy cherry desserts, these muffins are a delicious option: naturally gluten-free, dairy-free, and Paleo-friendly. They pair the deep flavor of unsweetened cocoa with bright, juicy cherries for a satisfying treat.
Why this recipe works
- Chocolate and cherries complement each other perfectly.
- Made with almond, tapioca and coconut flours for a gluten-free, Paleo-friendly texture.
- Allergy-friendly: soy-free, peanut-free, dairy-free and gluten-free.
- Easy to prepare and a crowd pleaser.
Recipe ingredients
- Almond flour – blanched almond flour yields a fine texture best for baking.
- Tapioca flour – adds chew and structure to gluten-free baked goods.
- Coconut flour – very absorbent; use only the amount called for.
- Coconut sugar – a lower-glycemic alternative to refined sugar.
- Unsweetened cocoa powder – for rich chocolate flavor.
- Baking soda – helps the muffins rise.
- Cream of tartar – improves texture and lift.
- Eggs – bind the batter and provide structure.
- Almond milk – use unsweetened, unflavored non-dairy milk.
- Olive oil – replaces butter for a dairy-free option; avocado oil also works.
- Chocolate chips – choose dairy-free or other varieties to suit your diet.
- Pitted cherries – fresh or frozen; frozen cherries can be used directly from the freezer.
See recipe card below for exact measurements and instructions.
Additions / Substitutions
- Swap tapioca flour for arrowroot powder if needed.
- Use brown sugar instead of coconut sugar (not Paleo if you do).
- Any unsweetened non-dairy milk can replace almond milk.
- Substitute avocado oil for olive oil if preferred.
Step by step instructions
Step 1: Preheat the oven to 350°F (175°C). Grease a 12-cup muffin tin or line with paper liners. In a large bowl, whisk together the almond flour, tapioca flour, coconut flour, coconut sugar, cocoa powder, baking soda, cream of tartar and salt until well combined.
Step 2: Add the eggs, almond milk and olive oil to the dry ingredients. Stir until the batter is smooth and evenly mixed.
Step 3: Fold in the chocolate chips and pitted cherries, being careful not to overmix. If using frozen cherries, add them straight from the freezer to avoid bleeding color into the batter.
Step 4: Evenly portion the batter into the prepared muffin tin and bake for 18–20 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs. Allow muffins to cool slightly in the tin, then transfer to a wire rack to cool completely.
Recipe FAQs
Yes. Add frozen pitted cherries directly into the batter without thawing.
Store cooled muffins covered at room temperature for up to 3 days, or refrigerate for longer freshness.
Yes. Once fully cooled, freeze muffins individually in freezer-safe bags or containers for up to 3 months.
Other Paleo Muffin recipes you’ll love
Paleo Gluten-Free Apple Crumb Muffins
Paleo Orange Cranberry Muffins
Paleo Chestnut Flour Gingerbread Muffins
Paleo Pumpkin Muffins
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Healthy Chocolate Cherry Muffins (Paleo, Gluten-free)
Ingredients
- 1 1/4 cups almond flour
- 1/2 cup tapioca flour (or arrowroot)
- 2 tbsp coconut flour
- 1/2 cup coconut sugar
- 1/2 cup unsweetened cocoa powder
- 1/2 tsp baking soda
- 1 tsp cream of tartar
- 1/2 tsp salt
- 2 large eggs
- 3/4 cup unsweetened almond milk (or other non-dairy milk)
- 1/2 cup olive oil (or avocado oil)
- 1/2 cup dairy-free chocolate chips
- 1 cup pitted cherries (fresh or frozen)
Instructions
- Preheat oven to 350°F (175°C). Grease a 12-cup muffin tin or line with liners.
- In a large bowl, combine the almond flour, tapioca flour, coconut flour, coconut sugar, cocoa powder, baking soda, cream of tartar and salt. Mix until blended.
- Add the eggs, almond milk and olive oil. Stir until the batter is smooth. Fold in the chocolate chips and cherries.
- Spoon the batter evenly into the muffin tin.
- Bake for 18–20 minutes or until a toothpick comes out clean. Cool in the tin briefly, then transfer to a rack to cool completely.
Notes
- Swap tapioca flour for arrowroot powder if needed.
- Brown sugar can replace coconut sugar but will not be Paleo.
- Use any unsweetened non-dairy milk in place of almond milk.
- Avocado oil can be used instead of olive oil.
Nutrition (per muffin, approximate)
- Calories: 296 kcal
- Carbohydrates: 23.4 g
- Protein: 5.9 g
- Fat: 22.8 g
- Sodium: 167 mg
Nutrition information is an approximation.
Additional Info
Course: Dessert
Cuisine: American
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