Win a $200 Amazon Gift Card by cooking this month’s recipe!

A healthier whole-wheat muffin recipe, these Dark Chocolate Muffins are bursting with chocolate chips and topped with crunchy almonds.

chocolate muffin topped with almonds and chocolate chips I have a serious thing for muffins, strawberry muffins, banana muffins, zucchini muffins, pumpkin muffins. What’s not to love?  Muffins work for breakfast, a snack, or even a healthier dessert in the case of these healthy chocolate muffins.  They are incredibly quick and easy to make, often requiring no more than two bowls and a spoon.  And they are freezer-friendly, making them a perfect grab-and-go breakfast.

One of my favorite things about muffins is that it’s easy to make them healthier… yet these muffins completely taste like an indulgence.  If I’m going to eat a muffin for breakfast or snack, I want to be sure it has some nutrition to it so I’m not just eating a cupcake disguised as a breakfast food.  (But it’s completely ok with me that I still feel like I’m eating a cupcake!)

healthy chocolate muffins in a muffin pan just out of the oven

This healthy muffin recipe is made with whole-wheat flour and flaxseed.  A full cup of applesauce keeps them moist, and honey acts as a natural sweetener to keep the muffins free of refined sugars.  The dark chocolate chips and cocoa powder not only make these breakfast muffins deliciously chocolatey, but also provide healthy antioxidants.  (Yes, I totally qualify chocolate as a health food.  You too?)

healthier chocolate muffins with almonds and chocolate chips with cup a tea


You can have one of these Chocolate Muffins ready for snacking in no time.  Simply mix up the dry and wet ingredients separately in two bowls, gently combine, and scoop the batter into a muffin tin.  Top with a few chocolate chips and chopped almonds, and bake.  Then it’s time to sit down, relax, and enjoy a few minutes to yourself!  You deserve it.

decorative image of chocolate muffins with almonds, sitting next to an apple and some tea with text title

Skinny Dark Chocolate Muffins

Servings: 12
Prep Time: 20 minutes
Cook Time: 15 minutes
Total Time: 35 minutes
A healthy chocolate muffin recipe that is refined sugar free and made with whole-wheat flour. A delicious breakfast muffin or snack.


  • 2/3 cup white whole-wheat flour
  • 1/3 cup all-purpose flour
  • ½ cup ground flaxseed
  • ½ cup cocoa powder
  • 1 tsp. baking powder
  • 1 tsp. baking soda
  • ½ tsp. salt
  • 2 eggs
  • 1 cup unsweetened applesauce
  • ½ cup milk
  • ¼ cup honey
  • 2 tbsp. brown sugar
  • 2 tsp. vanilla extract
  • ¼ cup 4 tbsp. unsalted butter, melted and cooled slightly
  • 1 cup dark chocolate chips, or chopped dark chocolate, divided
  • ½ cup chopped almonds, for topping


  • Preheat oven to 375 degrees F. Spray a muffin tin with cooking spray or line with paper liners.
  • In a large bowl, whisk together both flours, flaxseed, cocoa powder, baking powder, baking soda, and salt until well combined.
  • In a medium bowl, whisk together eggs, applesauce, milk, honey, brown sugar, and vanilla until well combined. Whisk in melted butter.
  • Pour the wet ingredients into the dry and stir until almost combined. You should still see some streaks of dry ingredients throughout. Gently stir in ¾ cup of the chocolate chips.
  • Scoop batter into the prepared muffin tin, dividing it evenly between the wells. Top with the remaining ¼ cup chocolate chips and chopped almonds, pressing them down gently onto the muffins.
  • Bake for 15-18 minutes, until a tester inserted in the center of a muffin comes out clean. Cool in the pan for 5 minutes and then transfer to a wire rack to cool completely.


Muffins can be stored in freezer for 3 months in sealed container or zip top bag. To defrost a muffin, use microwave defrost setting or let the muffin warm on the counter for 30 minutes. 
Calories: 287kcal, Carbohydrates: 32g, Protein: 7g, Fat: 16g, Saturated Fat: 8g, Cholesterol: 39mg, Sodium: 228mg, Potassium: 344mg, Fiber: 5g, Sugar: 16g, Vitamin A: 180IU, Vitamin C: 1mg, Calcium: 124mg, Iron: 2mg
Nutrition information is an estimate.
Course: Breakfast, Snack
Tried this recipe?Mention @kristines_kitchen on Instagram or tag #kristineskitchenblog.


This site contains affiliate links. If you make a purchase through these links, I may receive a small commission, at no extra cost to you. Thank you for supporting Kristine's Kitchen!