Chocolate Protein Muffins Recipe (Healthy & Low Carb!)


by Sil Pancho



Keto Food List



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Before I went low carb years ago, one of my favorite things in the world was a coffeehouse latte and a muffin for breakfast. In college, it was my favorite study snack – and no wonder I had no energy. Today’s double chocolate protein muffins recipe is inspired by those memories… but much healthier.

So much has changed since those days. But, even now – many years, two kids, and a business later – there’s something about enjoying a muffin with a steaming cup of keto coffee that’s just perfection. Except these days, it’s either keto blueberry muffins or low carb protein muffins.

I didn’t want to choose between chocolate protein muffins and chocolate chip protein muffins, so this recipe is both. Double chocolate protein muffins! And I feel so much better eating them than I did after those coffeehouse ones.

Baking with protein can create some dry results, but there’s a surprisingly simple solution: The sweetener! I use Besti Monk Fruit Allulose Blend because it measures just like sugar and locks in moisture — so you get a perfectly sweet muffin without the sugar spike.

What Are Protein Muffins?

Protein muffins have an added protein source that usually replaces some of the conventional flour in a traditional recipe.

Some protein powder muffin recipes use ingredients like Greek yogurt, oat flour, banana, or gluten-free flour, but this recipe uses low carb ingredients to keep them higher in protein and lower in sugar!

Why You’ll Love This Chocolate Chip Protein Muffin Recipe

  • Rich, double chocolate flavor
  • Moist, cakey texture (NOT rubbery or dry!)
  • 5 grams net carbs and 10 grams of protein per muffin
  • Prep in one bowl & bake in less than 30 minutes
  • The perfect snack or filling breakfast
  • Creates naturally keto and gluten-free muffins!
  • Double chocolate… need I say more?
Healthy protein muffin close up overhead

Ingredients You’ll Need

This section explains how to choose the best ingredients for healthy protein muffins, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.

  • Besti Monk Fruit Allulose Blend – Locks in moisture so these muffins stay moist and sugar-free! You can make them with another sweetener if you must, but know that they will turn out more dry.
  • Wholesome Yum Almond Flour – Another natural source of protein that keeps this recipe gluten free. The fine grind delivers a texture closer to traditional flour! Avoid using almond meal, or almond flour brands that are coarser.
  • Collagen Protein Powder – If you’ve seen my protein cookie dough bites or peanut butter protein cookies, you know I’m a huge fan of using collagen protein powder in low carb recipes. And this neutral powder makes a moist, cakey muffin, too. I prefer it over whey protein powder, but technically any unflavored protein powder will work in this recipe.
  • Cocoa Powder – A must for easy chocolate protein muffins! Cocoa powder imparts a richer chocolate flavor than using melted chocolate. Make sure it’s unsweetened, and I typically recommend Dutch processed cocoa powder, which is less bitter.
  • Baking Powder – Helps the muffins rise. Make sure it is fresh for best results. Don’t use baking soda, which is not the same and will yield a result that is bitter and does not rise.
  • Sea Salt – Balances the sweet taste in the muffins.
  • Coconut Oil – Keeps the muffins moist. You can also use butter or ghee. I don’t recommend substituting liquid oils, such as avocado oil, as this will change the texture of the end result.
  • Unsweetened Almond Milk – Helps the batter reach the right consistency. Feel free to substitute with your favorite keto milk, or make homemade almond milk. Make sure it’s at room temperature, to avoid solidifying the coconut oil when mixing.
  • Eggs – Use whole, large eggs, at room temperature for the same reason as the almond milk. Flax eggs might work for an egg-free option, but I have not tested this to confirm.
  • Vanilla Extract – Use the best quality vanilla you can.
  • Sugar-Free Chocolate Chips – Turns these into chocolate chip protein muffins! You can also use a chopped sugar-free dark chocolate bar.
Protein muffin recipe ingredients in bowls

How To Make Protein Muffins

This section shows how to make protein breakfast muffins with step-by-step photos and details about the technique. For full instructions, see the recipe card below.

  • Mix dry ingredients. Mix almond flour, Besti, cocoa powder, baking powder, salt, and protein powder in a large mixing bowl.
  • Add wet ingredients. Stir in melted coconut oil and almond milk, followed by eggs and vanilla. Fold in chocolate chips.
Dry ingredients for muffins in a bowl
Protein muffin recipe batter with wet ingredients and chocolate chips added

  • Scoop. Transfer muffin batter to a lined muffin tin, filling cups evenly. Add additional chocolate chips on top, if desired.
  • Bake. Bake until an inserted toothpick comes out clean. Let muffins cool on a cooling rack for the best texture.
Muffin batter spooned into muffin tin
Finished protein powder muffins unwrapped and removed from baking pan

Tips For The Best High Protein Muffins

Baking with protein can create different results than recipes with conventional flour, so follow these tips for best results.

  • Expect a thick batter. It will be thicker than traditional muffin recipes, but this is normal.
  • Use the right sweetener. To avoid a dry muffin, use a an allulose-based sweetener, like Besti, instead of sugar alcohols such as erythritol. (Most brands of monk fruit and stevia also are erythritol-based. Besti is not, and keeps baked goods moist.)
  • Cool completely. The texture is better this way, but you can easily warm them up later.
  • Add chocolate chips in the batter and on top. It’s optional, but makes them look extra nice.

Frequently Asked Questions

Answering a few quick FAQs…

Are protein muffins good for you?

Not all easy protein muffin recipes are good for you, since they can still contain added sugar or starches you may want to avoid. But these low carb protein muffins are definitely good for you, with no sugar, grains, or artificial ingredients.

How to make protein muffins moist?

There are several things you can do to keep muffins more moist:

  • Use enough fat. Fat adds moisture, and keeps the muffins more satisfying.
  • Use the best sweetener. Besti sweetener helps muffins retain moisture.
  • Choose a better protein source. A collagen-rich protein source keeps the recipe more chewy and rich, instead of dry or rubbery.

Can I make protein muffins with whey?

Whey is a common ingredient choice for protein powder muffins, but it is not the best for flavor or texture. I recommend a collagen protein for better results! However, you can still try these with whey if that’s what you have.

Can I use coconut flour?

Sorry, no. The properties of coconut flour are too different from almond flour to suggest a replacement. If you have a nut allergy, sunflower seed meal might work, but the flavor and texture will be different.

Storage Instructions

Store muffins on the counter for a few days, or in the fridge for 7 to 10 days.

Can you freeze protein muffins?

Yes, you can! Cool completely, then cover tightly and freeze for up to 1 month.

They are best reheated afterward (either in the microwave or a warm oven), but they will taste delicious no matter what.

Protein muffin split in half

More Protein Powder Desserts

Looking to sneak more protein into you treats? Try these recipes!


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Tap on the times in the instructions below to start a kitchen timer while you cook.

  1. Preheat the oven to 350 degrees F (177 degrees C). Line a muffin pan with 12 parchment paper liners or silicone muffin liners.

  2. In a large bowl, stir together the almond flour, sweetener, cocoa powder, collagen, baking powder, and sea salt.

  3. Stir in the melted coconut oil and almond milk. Whisk in the eggs and vanilla. Fold in the chocolate chips last. (If you’d like, you can reserve 1/4 cup of the chocolate chips to add on top.)

  4. Scoop the batter evenly into the muffin cups, filling almost full. If you reserved some chocolate chips in the previous step, sprinkle them on top and press gently into the batter.

  5. Bake for about 25 minutes, until the tops are slightly darker on the edges and an inserted toothpick comes out clean.

Recipe Notes

Serving size: 1 muffin

Nutrition Facts

Amount per serving. Serving size in recipe notes above.

Calories 233

Fat 20g

Protein 10g

Total Carbs 10g

Net Carbs 5g

Fiber 5g

Sugar 0g

Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.

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