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A head on image of a chocolate chip coffee muffin with a bite taken out of it surrounded by coffee beans
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5 from 3 votes

Chocolate Chip Coffee Muffins - Clean Eating, Gluten Free!

With a classic, domed top, and a gorgeously soft and light inner crumb that's studded with pockets of warm dark chocolate, these coffee-infused muffins are the perfect gluten-free afternoon pick me up or a great way to kick start your day!
Prep Time10 mins
Cook Time30 mins
Total Time40 mins
Course: Breakfast, Dessert, Snack
Cuisine: American
Servings: 12
Calories: 306kcal
Author: Kitrusy



  • Prep: Preheat oven to 425°F and thoroughly grease your 12-count muffin tins with butter or line them with paper liners.
  • Make the Muffin Batter: To a large bowl, add the almond flour, gluten-free flour blend* (see notes), nutmeg, baking powder, salt, and coconut sugar. Mix everything together until thoroughly combined.
  • Mix your instant coffee granules* (see notes) into your milk until mostly dissolved.
  • Make a well in the middle of the dry ingredients and add the coffee/milk mixture, along with the eggs, oil, and vanilla. Mix everything together until your batter is fully combined and then fold in the chopped chocolate.
  • Divide your batter between your prepared muffin tins.
  • Bake at 425°F for the first 5 minutes, and then, without opening the oven, drop the temp down to 350°F and bake for 20-25 min until a toothpick comes out clean.
  • Remove from the oven and allow your muffins to cool for 5-10 minutes in the tins before unmolding them.
  • Storage: Enjoy your muffins and store any leftovers in an airtight container either at:
    Room temperature for up to 5 days
    In the fridge for up to 10 days
    In the freezer for up the three months. - To reheat, you can remove your muffins from the freezer and allow them to thaw overnight in the fridge, or at room temperature for an hour or from frozen, you can reheat them in the microwave for 20-30 seconds.


  • I'm using King Arthur's Gluten Free Measure-for-Measure flour, You can also use:
    • Bob's Red Mill 1-1 Gluten Free Flour Blend or
    • Replace the amount of GF flour blend with almond flour but reduce the liquid by 1-2 tbsp or
    • if you're not gluten-free, you can use either white whole wheat flour or whole-wheat pastry flour, reduced by 1-2 tbsp.
  • If you want to use freshly brewed coffee in place of instant coffee, you can do so by strongly brewing your coffee in 1/3 cup of water and adding 1/3 cup milk to it.
  • In addition to chopping the chocolate into irregular shards and chunks, you can also use a mixture of cocoa percentages such as 60% and 80%.


Serving: 1muffin | Calories: 306kcal | Carbohydrates: 25g | Protein: 7g | Fat: 21g | Saturated Fat: 4g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 6g | Trans Fat: 0.01g | Cholesterol: 33mg | Sodium: 86mg | Potassium: 234mg | Fiber: 4g | Sugar: 10g | Vitamin A: 71IU | Vitamin C: 0.001mg | Calcium: 119mg | Iron: 3mg