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These Air Fryer chocolate protein muffins are soft, moist, naturally sweetened, and packed with protein. Cottage cheese, eggs, oats, and dark chocolate chunks come together in these easy muffins that are perfect for meal prep (just like my Air Fryer banana muffins), breakfast on the go, or an afternoon snack when you’re craving something chocolatey.

The best part? Everything comes together in the food processor, making cleanup incredibly easy.

Sneaking extra protein into everyday foods is something I have been consciously doing over the last few years. I always make it a point to start my day with a high protein breakfast like Air Fryer sausage patties and Air Fryer scrambled eggs.

This time, I wanted to give my favorite chocolate breakfast muffins an extra protein boost, and that’s when I tried this recipe.

Quick Look At This Recipe

Flavor: Soft, moist and chocolatey with a hint of cinnamon.

⏱️ Prep time: 5 minutes.

🔥 Cook time: 12-13 minutes.

⏲️ Total time: 18 minutes.

👥 Servings: 12 muffins.

🥄 Tools: Air Fryer, silicone liners, food processor.

❄️ Freezer friendly: No, but just like my Air Fryer chocolate chip muffins, these can be refrigerated for up to a week.

👩🏻‍🍳 Tip: Reserve some chocolate chunks for the tops of the muffins for a bakery-style finish.

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Why You’ll Love This Recipe

  • These muffins come together in just under 20 minutes and are perfect to batch-make ahead of time- like my Air Fryer 2 ingredient pumpkin muffins.
  • They’re naturally gluten-free and packed with protein.
  • The recipe uses no refined flour, and the muffins are sweetened with honey!
Pic of Jen Gamble

Recipe Ingredients

  • Old fashioned rolled oats: The base of the muffins- I used gluten free ones here.
  • Eggs: To bind everything and add structure to the muffins. And of course, for the protein.
  • Cottage cheese: For extra protein and to keep the muffins soft and moist.
  • Baking powder: The leavening agent.
  • Honey: For sweetness. You can also just stick to using sugar- like I do when I make my Air Fryer blueberry muffin bites.
  • Cinnamon: Ground cinnamon, to balance out the sweetness and add some depth.
  • Chocolate chunks: 72% cacao, for that deep, chocolatey deliciousness.

See recipe card for quantities.

Variations

  • Stir in some chopped pecans, walnuts or almonds to lend some extra texture and a bit of crunch to the protein muffins.
  • Try white chocolate chips, milk chocolate chips, or peanut butter chips for a different flavor profile.
  • Use chopped fresh fruit like strawberries (like I used in my Air Fryer strawberry French toast roll ups), blueberries or raspberries along with the chocolate chunks.
  • For a richer, chocolatey flavor, you can also add a teaspoon of unsweetened cocoa powder into the mix.

How to Make Air Fryer Chocolate Protein Muffins

  1. Add all ingredients except chocolate chunks to a food processor.
  1. Pulse until the mixture is smooth and fully combined.
  1. Transfer to a bowl and add in the chocolate chunks. Stir.
  1. Pour into silicone muffin moulds and top with extra chocolate chunks. Air fry at 325 degrees for 12 minutes.

Serving Ideas & Suggestions

Serve these air fried chocolate protein muffins warm with a drizzle of peanut butter or almond butter and some fresh berries if you’re making these for breakfast. I always do this when I make my favorite Air Fryer frozen French toast sticks or Air Fryer oatmeal.

You can also enjoy one of these muffins as-is, as a quick post workout snack that also satisfies your sweet tooth.

Recipe Tips & Tricks

  • Don’t preheat the Air Fryer. These chocolate protein muffins are best
  • Allow the muffins to cool down completely before you serve.
  • Once you add in the chocolate chunks, don’t overmix the batter. I always keep this in mind when I make my baked foods- especially my Air Fryer soft pretzels.
  • Every Air Fryer works differently, so make sure you check the muffins around the 12 minute mark to see if they are done. If they pass the toothpick test, get them out and let them cool.
  • Remember to grease the silicone moulds with some cooking spray before you pour in the muffin batter. This will help the muffins glide out easily- I did this when I made my Air Fryer lemon poppy seed muffins too.

Recipe FAQs

How do I store leftover Air Fryer chocolate protein muffins?

You can store the leftover chocolate protein muffins in an airtight container and refrigerate for up to 4 days.

Can I use regular oats to make Air Fryer chocolate protein muffins?

Yes, you can use regular rolled oats too if you’re not sensitive to gluten.

How will I know the chocolate protein muffins are done?

Insert a toothpick in the middle of a muffin at the 12 minute mark. If the toothpick comes out clean, the muffins are done cooking.

More Air Fryer Sweet Breakfast Recipes

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chocolate chip protein muffins on a white plate
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Servings: 12 servings

Air Fryer Chocolate Protein Muffins

By Jen Gamble
These Air Fryer Chocolate Protein Muffins are soft, moist, protein-packed, and naturally sweetened. They're perfect for breakfast, snacking, or meal prep.
Prep: 5 minutes
Cook: 12 minutes
Total: 17 minutes
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Ingredients 

  • 1 1/2 cups gluten-free old-fashioned rolled oats
  • 1 cup cottage cheese
  • 2 eggs
  • 2 tsp baking powder
  • 1 tsp cinnamon
  • 1/4 cup honey
  • 2/3 cup chocolate chunks, 72% cacao

Instructions 

  • Add oats, cottage cheese, eggs, baking powder, cinnamon, and honey to a food processor.
  • Blend until smooth and fully combined.
  • Transfer batter to a bowl and fold in most of the chocolate chunks, reserving ¼ cup.
  • Fill silicone muffin liners with about 1½ tablespoons of batter each.
  • Top with the remaining chocolate chunks.
  • Air fry on BAKE mode at 325°F for 12-13 minutes.
  • Cool completely before serving.
  • Store leftovers in an airtight container in the refrigerator for up to one week.

Notes

  • Check the muffins early if your Air Fryer runs hot.
  • For extra chocolate flavor, use dark chocolate chunks with 70% cacao or higher.
  • These muffins can be frozen for up to 3 months.

Nutrition

Calories: 143kcal, Carbohydrates: 19g, Protein: 5g, Fat: 6g, Saturated Fat: 3g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 2g, Trans Fat: 0.01g, Cholesterol: 31mg, Sodium: 138mg, Potassium: 123mg, Fiber: 2g, Sugar: 10g, Vitamin A: 69IU, Vitamin C: 0.04mg, Calcium: 71mg, Iron: 1mg

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

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Jen Gamble

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