Protein Muffins

Jump to recipeThese easy protein muffins are moist, rich, super chocolaty, healthy and refined sugar free! They are quick to prepare and need just one bowl.

By Maya Krampf

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

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

Why You’ll Love These Protein Muffins

Rich, double chocolate flavor
Moist, cakey texture (NOT rubbery or dry!)
10 grams of protein and 5 grams net carbs 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

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.

Chocolate protein powder muffins with almond flour and Besti

Get Besti For This Recipe Here

Ingredients & Substitutions

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.

Some protein 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!

Besti Monk Fruit Allulose Blend – Locks in moisture, so these high protein 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. Coconut flour is too dry and does not make a good substitute, but if you have a nut allergy, sunflower seed meal might work.
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, to help you visualize it. For full instructions, including amounts and temperatures, 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.

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 the protein muffins until an inserted toothpick comes out clean. Let them cool on a cooling rack for the best texture.

Finished protein powder muffins unwrapped and removed from baking pan

Tips For The Best 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.

Recipe Variations

Want a different flavor? Try some of these other flavor variations:

Banana – Make banana protein muffins by replacing the cocoa powder with 1 mashed ripe banana and an extra 1/4 cup of almond flour. Reduce the almond milk to 1/4 cup.
Blueberry – Replace the cocoa powder with 1/2 cup additional almond flour, omit the chocolate chips, and add 1 cup of fresh or frozen blueberries to the batter to make blueberry protein muffins. (You can also try my almond flour blueberry muffins instead.)
Pumpkin – Replace the cocoa powder with 1/2 cup additional almond flour, replace the almond milk with 3/4 cup of pumpkin puree, and add 1/2 tablespoon of pumpkin pie spice. You can use the chocolate chips or omit them. (Or, try my almond flour pumpkin muffins instead.)

Storage Instructions

Store: You can keep protein muffins on the counter for a few days, or in the fridge for 7 to 10 days.
Freeze: 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, with a little butter on top), but they will taste delicious no matter what.

More Protein Powder Desserts

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

Muffin Tin – Can’t make muffins without one! I like that this one cleans easily if any batter gets outside the liners.
Parchment Muffin Liners – Nothing sticks to these. Don’t confuse them with regular paper liners; the parchment ones are much better.

Protein Muffin Recipe

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