Protein Muffins
Published Jul 06, 2026
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These moist strawberry protein muffins are easy to make and delicious as a light breakfast, lunchbox treat, or meal prep snack. They’re made with almond and oat flour, sweetened with applesauce, and bulked up with cottage cheese, Greek yogurt, and protein powder. Swap the berries with your favorite mix-ins!
Easy Protein Muffins Recipe
I gave my applesauce muffins a high-protein boost! Some protein muffin recipes throw protein powder into the mix and call it a day. But for this recipe, I’ve used multiple sources of protein, including vanilla protein powder, cottage cheese, Greek yogurt, and almond and oat flours. The result is flavorful, moist protein muffins that are as delicious as they are filling, perfect for a light breakfast or quick snack throughout the day. I love that they store and freeze well, too, making them great to make ahead and pack in lunch boxes.
I’ve always added protein powder to protein shakes, but lately I’ve been loving the extra protein in my protein oatmeal and protein pancakes recipes, too. And these protein muffins couldn’t be easier. You can even make them as mini muffins!
Key Ingredients
With a few simple ingredient swaps, this recipe makes a batch of protein-packed muffins that you can fill with fresh berries or any mix-ins you’d like. Scroll down to the recipe card for the exact amounts for each ingredient.
- Applesauce – You’ll want to use unsweetened applesauce, either store-bought or homemade.
- Eggs – Room temperature eggs are easier to mix.
- Cottage Cheese – I love using cottage cheese in cottage cheese pancakes and cottage cheese flatbread. It’s an underrated ingredient that adds plenty of moisture and protein without impacting the flavor of these muffins.
- Greek Yogurt – Sour cream is a good substitute.
- Sugar – When I tested this recipe with just the applesauce as a sweetener, I found the flavor a bit flat. A little bit of granulated or brown sugar does the trick, or you could use honey.
- Vanilla – Please use real vanilla extract or vanilla paste, and not imitation.
- Oat Flour – Oat flour is one of my favorites for gluten-free baking. It’s perfect for light, tender muffins. You can also make oat flour yourself! Just add oats to a high-powered blender and pulse until you have a fine powder.
- Almond Flour – Another gluten-free flour alternative that also adds protein.
- Vanilla Protein Powder – You can use your favorite, either whey or plant-based. Swap vanilla with chocolate protein powder if you’d like.
- Baking Powder – Not the same thing as baking soda. Make sure it’s fresh!
- Strawberries – Chop the strawberries into small pieces, and leave them to dry on a paper towel for a few minutes. This releases some of the moisture so it doesn’t find its way into the muffin batter. Instead of strawberries, you could also make blueberry cottage cheese muffins, chocolate chip protein muffins, or add more mix-ins like dried fruit and nuts.
Baking With Protein Powder
Since protein powder is a bit like flour, it absorbs moisture, so it shouldn’t be added to baked goods unless it’s called for in a recipe. When used correctly, it’s a wonderful way to add protein and flavor. In addition to these protein muffins, I love adding protein powder to protein waffles and baked oatmeal.
Tips for the Best Protein Muffins
- Avoid bits of cottage cheese. Blend the cottage cheese with the other wet ingredients until smooth, so that no clumps or specks remain.
- Use full-fat ingredients. I tested this recipe with full-fat Greek yogurt and cottage cheese. I haven’t tried low-fat options.
- Almond flour vs. almond meal. Both will work in this recipe. Almond meal is a coarser, less-fine version of almond flour. The muffins may look a bit different depending on which one you use, but they’ll taste great either way.
- Rest the batter before you bake. It rehydrates the flour and makes these gluten-free protein muffins extra light and tender.
- Don’t underbake. These protein muffins bake up darker than traditional muffins due to the oat flour and protein powder in the recipe. So if they look a bit darkened, chances are, they’re not overbaked. Test them using a toothpick. When it comes out clean, they’re done.
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Protein Muffins
Ingredients
- 5 tablespoons unsweetened applesauce
- 2 large eggs
- ½ cup cottage cheese
- ¼ cup Greek yogurt
- ¼ cup sugar
- 1½ teaspoons pure vanilla extract
- ⅔ cup + 3 tablespoons oat flour
- ½ cup almond flour
- 2 scoops vanilla protein powder
- 2 teaspoons baking powder
- ¼ teaspoon salt
- ¾ cup fresh strawberries, chopped
Instructions
- Heat the oven. First, preheat your oven to 350ºF and line a 12-cup muffin pan with paper liners.
- Combine the wet ingredients. Add applesauce, eggs, cottage cheese, yogurt, sugar, and vanilla extract to a food blender. Blend on high speed until the cottage cheese is smooth and everything is well blended.
- Combine the dry ingredients. In a large mixing bowl, whisk together the oat flour, almond flour, vanilla protein powder, baking powder, and salt.
- Fold in the wet ingredients. Stir the wet ingredients into the dry ingredients just until combined; do not overmix. Set it aside and let the batter rest for 10 minutes before folding in the chopped strawberries. You can leave some extra strawberries to add to the tops of the muffins.
- Bake the muffins. Transfer the muffin pan to the oven and bake the protein muffins for 25 minutes or until a toothpick inserted in the center of a muffin comes out clean. Due to the oat flour and vanilla protein powder, they may look a bit darker than regular muffins.
- Cool, then serve. Cool the muffins before removing them from the pan and serving.
Equipment
Notes
- Chop your strawberries and leave them to dry for a few minutes. This will prevent the muffins from being too wet or soggy.
- Blend your cottage cheese until the chunks or curds are smooth.
- I used full-fat yogurt for the recipe. I did not test with lower-fat options, so I do not know how they may work.
- You can use almond flour or almond meal. The appearance may be a bit different, but it will not impact the flavor.
- Make sure you rest your batter so the oat flour rehydrates properly.
Nutrition
Nutritional info is an estimate and provided as courtesy. Values may vary according to the ingredients and tools used. Please use your preferred nutritional calculator for more detailed info.
How to Make Strawberry Protein Muffins
- Blend the wet ingredients. Add the applesauce, eggs, cottage cheese, and yogurt to a blender with the sugar and vanilla. Blend until there aren’t any curds of cottage cheese remaining.
- Combine the dry ingredients. Meanwhile, whisk the oat flour, almond flour, protein powder, salt, and baking powder in a bowl.
- Mix and rest the batter. Fold the blended wet ingredients into the dry ingredients. Let the batter rest for 10 minutes before folding in the strawberries. I usually set aside a few strawberry chunks to garnish the tops of the muffins before baking.
- Bake. Divide the batter between the lined wells of a 12-well muffin tin. Before baking, I’ll usually press a few reserved strawberry pieces into the tops of the muffins. Bake the muffins at 350ºF for 25 minutes, or until a toothpick comes out clean. These protein muffins should cool completely in the pan before you serve or store them.
Mini Muffins
To bake the batter in a mini muffin pan instead, you’ll need to shorten the baking time to 10-14 minutes. The oven temperature can stay the same (350ºF). I recommend filling the muffin wells ¾ full, which is about 1-2 tablespoons of batter per liner.
Storage and Freezing
- Store at room temperature. Wait until these protein muffins have completely cooled before storing, or they may get soggy. Seal them in a container or a resealable bag to keep in a cool, dry location.
- Freeze for up to 2 months. Store the cooled muffins in a large freezer bag or freezer-safe container. These protein muffins thaw relatively quickly at room temperature. Perfect for a grab-and-go breakfast or snack!
