By All the deep, near-black chocolate of the Costco bakery muffin, with 11g of protein and 23g of sugar instead of 48g. Cottage cheese is doing the heavy lifting, there's a full chopped chocolate bar folded through, and there's no protein powder anywhere.
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The tops dome up tall and crackly. The crumb is dark and properly moist. And they hold up in the freezer for months, which is the whole reason I make a double batch.
If you already make our blueberry protein muffins, this is the same idea pushed as far as it goes, and there's a whole pile more protein muffin recipes where this came from 🍫
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what changed from the Costco version
Here's the comparison, per muffin. Protein: 11g, up from 10g. Sugar: 23g, down from 48g. Fat: 14g, down from 38g. Fiber: 6g, up from 3g. Calories: 351, down from 690.
One thing worth being straight about: the Costco muffin is a genuinely enormous 167g, and these come in around 125g. So some of that calorie gap is just size.
The number that doesn't care about size is protein per 100 calories, and that's 3.13 against their 1.45. More than double, from actual food.
Most of the difference comes from three places. Cottage cheese replaces a chunk of the fat and brings protein with it. A chopped dark chocolate bar goes in instead of two full cups of semi-sweet chips, so you get bigger melty pools with less sugar. And maple syrup carries most of the sweetening instead of a cup and a quarter of granulated 🙌
key ingredients & swaps
All substitutions are a 1:1 substitute unless otherwise noted. See the recipe card for quantities.
- Cocoa powder: Use what ya got!
- All-purpose flour: A 1:1 gluten-free swap works here.
- Almond flour: Adds healthy fats and keeps the texture tender and moist.
- Ground flax seeds: Hemp seeds or chia work too. There's less flax in these than in our other muffins because the cocoa is already bringing plenty of fiber.
- Blended cottage cheese and Greek yogurt: The protein and a lot of the moisture.
- Unsweetened applesauce: In place of the butter you'd normally see in a muffin this rich. It keeps them moist and takes a real bite out of the fat. Melted butter works too.
- Eggs: Binds everything and adds protein.
- Maple syrup and brown sugar: The maple does most of the sweetening. The brown sugar is small, but it adds a caramel note that keeps the cocoa from tasting flat.
- Avocado oil: Neutral oil that gives a super soft texture. Canola or vegetable oil works too.
- Chopped dark chocolate: I prefer a bar, but chips work too.
- Hot coffee or milk: Always add at the very end to wake everything up.
This recipe has not been tested with other substitutions or variations. If you replace or add any ingredients, please let us know how it turned out in the comments below!
step by step: tips to nail this recipe every time
- Rest the batter 15 minutes: The flax and the cocoa both need time to drink up liquid. This is the step that keeps them from baking dry.
- Hot milk/coffee goes in last, and stream it: Pouring it in all at once can spot-cook the eggs. Stream and stir gently.
- Only fill every other muffin cup: This is how you get tall domes instead of flat spread.
- Fill them very full: Almost overflowing. If that makes you nervous, make 20 to 24 normal muffins instead and eat two.
quick recipe video
the #1 tip: the hot liquid goes in last
This is the one that makes or breaks it. Most recipes have you whisk the cocoa in with the flour and move on. Do that here and you'll get a muffin that tastes vaguely chocolatey and looks brown.
Instead, mix your whole batter first. Then stream in the hot milk at the very end. Cocoa's best flavor lives in compounds that dissolve in fat, not water. By the time you add the hot liquid, the oil is already in the bowl, so the heat pulls out far more than it could on its own. The batter visibly darkens as you stir it in.
The 15 minute rest before that is the same idea in reverse: ground flax absorbs several times its weight in liquid, and cocoa soaks up roughly twice what the flour it's replacing would. Mix and bake immediately and both keep pulling moisture out of the crumb in the oven. That's the classic dry chocolate muffin, and it's the most common complaint on copycat versions of this recipe.
reader questions (optional)
Not at all, and the recipe as written uses hot milk anyway. If you do use coffee, it works out to roughly 3mg of caffeine per muffin, which is about what is in a cup of decaf.
Yes, with a 1:1 gluten-free flour blend.
Yes. Fill them very full and take 3 to 4 minutes off the bake time.
troubleshooting & testing notes
Give em' room
Filling every muffin cup makes them spread instead of rise. Leaving space between is the whole trick, same as our lemon muffins.
You can't see when they're done
Dark batter gives you no browning cue at all, which is how chocolate muffins end up overbaked. A toothpick should come out with moist crumbs and nothing wet. Pull them a touch early rather than late.
Let em' cool
The chocolate chunks stay molten well past the point where the crumb is actually done. Pulling one apart at 10 minutes will read underbaked when it isn't. Give them the full 30.
how to store & meal prep it
These freeze like a dream, which is the whole reason I make a double batch!
- Room temp: Airtight container on the counter up to 5 days. I don't recommend the fridge.
- Freezer: Sealed bag or container up to 3 months. Defrost overnight or microwave straight from frozen 30 seconds at a time.
- Reheating: Microwave 15 to 30 seconds, or a toaster oven for 3 to 5 minutes. Warm is when the chocolate goes molten again.
- How I serve them: Split warm with a spoonful of Greek yogurt on top, or alongside eggs or breakfast meatballs for a breakfast that holds you until lunch.
Recipe
double chocolate protein muffins (Costco copycat, no protein powder)
Ingredients
dry
- 1-⅓ cups all-purpose flour (reserve 1 tablespoon for the chocolate)
- ⅔ cup Dutch-process cocoa powder
- ½ cup almond flour
- ¼ cup ground flax seeds
- 2-½ teaspoon baking powder
- ¾ teaspoon baking soda
- ¾ teaspoon salt
wet
- 1-½ cups cottage cheese (blended, measured before blending)
- ½ cup unsweetened applesauce
- 3 eggs
- 1 tablespoon vanilla extract
- ¾ cup maple syrup
- 2 tablespoon brown sugar
- ⅓ cup Greek yogurt (plain, non-fat)
- ⅓ cup avocado oil
added last
- ⅓ cup hot milk (or hot coffee)
chocolate
- 1-¼ cups chopped dark chocolate, 60 to 70% (or chips)
Before you start!
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Instructions
- Preheat oven to 425°F and line a muffin tin with aluminum liners. This batter likes to stick so best to use parchment paper liners or aluminum ones.
- Chop the 1-¼ cups chopped dark chocolate, 60 to 70% into bits.
- Whisk the 1-⅓ cups all-purpose flour, ⅔ cup Dutch-process cocoa powder, ½ cup almond flour, ¼ cup ground flax seeds, 2-½ tsp baking powder, ¾ tsp baking soda, and ¾ tsp salt.
- Lightly blend together 1-½ cups cottage cheese, ½ cup unsweetened applesauce, 3 eggs, 1 tbsp vanilla extract, ¾ cup maple syrup, 2 tbsp brown sugar, ⅓ cup Greek yogurt, and ⅓ cup avocado oil. Don't overblend!
- Add the wet ingredients to the dry ingredients and stir. Some flour streaks are ok. Rest the batter 15 minutes. The flax and cocoa need this time to hydrate, and skipping it is what makes chocolate muffins bake dry.Fold in the chocolate chunks. Save some for the top of the muffins.
- Heat the ⅓ cup hot milk (or coffee) until steaming. Stream it into the batter, stirring just until it comes together. The batter will loosen and go visibly darker.
- Scoop immediately into the lined tin, filling only every other cup, very full and domed. Work in two batches.
- Bake at 425°F for 10 minutes, then reduce to 350°F and bake 15 to 18 more without opening the oven.
- Cool in the pan 10 minutes, then transfer and cool completely, about 30 minutes, for the centers to finish setting. If you try to peel back the liners while they are still warm they will stick a lot! Especially paper ones. Remember to increase the oven temperature again before baking the second batch!
Video
Notes
Looking for more information?
Additional substitution information can be found above in the substitution section of this post.
Nutrition Disclaimer
Nutritional information is an estimate and for informational purposes only.
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