These Blueberry Cream Cheese Protein Muffins are fluffy, delicious, and packed with goodies! They mix juicy blueberries with creamy cheese for a delightful snack that’s also good for you.
Bake a batch for breakfast and enjoy them any time! I love grabbing one before a workout for a tasty boost—plus, who can resist that creamy surprise inside? Yum!
Key Ingredients & Substitutions
Almond Flour: This nutty flour gives a great texture. If you’re allergic, oat flour is a good substitute, making the muffins fluffier. Both options are gluten-free!
Protein Powder: I love using vanilla protein powder for added flavor, but you can use plain if you prefer. Just check that it blends smoothly with the other ingredients.
Greek Yogurt: It adds moisture and protein! Unsweetened applesauce is a great alternative if you’re looking for something lower in fat. Both keep the muffins tender.
Blueberries: Fresh blueberries shine here! If they’re out of season, frozen ones work too—just be sure to thaw and drain them to avoid soggy muffins.
Cream Cheese: Using regular cream cheese makes these muffins rich, but you can swap in low-fat cream cheese or Greek yogurt for a lighter option without losing creamy goodness.
How Do I Fold Blueberries without Crushing Them?
Gently folding in blueberries is key to keeping them whole. Here’s how:
- After mixing wet and dry ingredients, add blueberries last.
- Use a spatula or wooden spoon, and scoop from the bottom of the bowl to the top, gently folding the batter over the blueberries.
- Be gentle! Mix just until evenly distributed to avoid smashing them.
This prevents the blueberries from breaking apart, keeping those lovely bursts of flavor in every bite!
What’s the Best Way to Create a Cream Cheese Center?
To get that creamy filling, it’s important to layer correctly:
- Start with 1 tablespoon of muffin batter in each cup.
- Add 1 teaspoon of the cream cheese mixture right in the center of the batter.
- Top it off with more batter to cover the cream cheese completely.
This layering keeps the cream cheese surrounded, ensuring you get a delightful surprise in the middle of each muffin!
These helpful tips will make baking your Blueberry Cream Cheese Protein Muffins easy and fun! Enjoy your muffins!

Blueberry Cream Cheese Protein Muffins
Ingredients You’ll Need:
For the Muffins:
- 1 1/2 cups almond flour (or oat flour)
- 1/2 cup vanilla or plain protein powder (whey or plant-based)
- 1 tsp baking powder
- 1/4 tsp baking soda
- 1/4 tsp salt
- 2 large eggs
- 1/3 cup plain Greek yogurt or unsweetened applesauce
- 1/4 cup honey or maple syrup
- 1 tsp vanilla extract
- 1/4 cup unsweetened almond milk (or any milk)
- 1 cup fresh blueberries (can use frozen, thawed and drained)
For the Cream Cheese Filling:
- 4 oz cream cheese, softened
- 2 tbsp Greek yogurt or sour cream
- 1 tbsp honey or sweetener of choice
- 1/2 tsp vanilla extract
How Much Time Will You Need?
This recipe takes about 15 minutes to prepare, plus an additional 20-25 minutes for baking. You’ll have delicious muffins ready in about 40 minutes—perfect for a quick breakfast or snack!
Step-by-Step Instructions:
1. Preheat the Oven:
Start by preheating your oven to 350°F (175°C). Prepare a 12-cup muffin tin by lining it with paper liners or greasing it with cooking spray to prevent sticking.
2. Mix the Dry Ingredients:
In a large bowl, combine the almond flour, protein powder, baking powder, baking soda, and salt. Whisk them together until they’re well mixed and no lumps remain.
3. Combine Wet Ingredients:
In a separate medium bowl, crack the eggs and beat them. Next, add the Greek yogurt (or applesauce), honey, vanilla extract, and milk. Mix everything until it’s smooth and well combined.
4. Combine Dry and Wet Ingredients:
Pour the wet ingredients into the bowl with the dry ingredients. Stir gently until just combined—be careful not to over-mix, as we want the muffins to be fluffy!
5. Fold in the Blueberries:
Gently fold the blueberries into the batter using a spatula. Try not to smash them; a gentle touch will keep the berries intact and juicy!
6. Prepare the Cream Cheese Filling:
In a small bowl, mix together the softened cream cheese, Greek yogurt, honey, and vanilla extract. Stir until the mixture is smooth and creamy.
7. Assemble the Muffins:
Using a spoon, add about one tablespoon of muffin batter to each muffin cup. Next, add a teaspoon of the cream cheese filling on top of the batter in each cup. Finally, spoon more batter on top to completely cover the filling.
8. Add Optional Blueberries:
For a nice touch, you can sprinkle a few extra blueberries on top of each muffin before baking.
9. Bake the Muffins:
Place the muffin tin in the preheated oven and bake for 20-25 minutes. Check if they’re done by inserting a toothpick into the muffin (not the cream cheese center); it should come out clean.
10. Cool the Muffins:
Once baked, let the muffins cool in the pan for about 5 minutes. Then transfer to a wire rack to cool completely.
11. Serve and Enjoy:
These muffins are delightful served warm or at room temperature. For an extra treat, you can top them with cream cheese or a dollop of butter before enjoying!
Now you have a delicious batch of moist, protein-packed blueberry muffins with a creamy center. Perfect for starting your day off right or as a healthy snack throughout the day!
Can I Use Other Types of Flour?
Yes, you can substitute almond flour with oat flour, coconut flour, or whole wheat flour. However, keep in mind that coconut flour absorbs more moisture, so you may need to adjust the liquid in the recipe accordingly.
How Should I Store Leftover Muffins?
Store leftover muffins in an airtight container at room temperature for up to 3 days. You can also refrigerate them for up to a week, or freeze them for longer storage—just make sure to wrap them well to prevent freezer burn.
Can I Replace the Eggs in This Recipe?
Absolutely! If you’re looking for an egg substitute, you can use 1/4 cup of unsweetened applesauce or a flax egg (1 tablespoon ground flaxseed mixed with 2.5 tablespoons water) for each egg.
How Do I Ensure My Blueberries Don’t Sink?
To prevent blueberries from sinking to the bottom, you can toss them in a little bit of flour before folding them into the batter. This helps create a light coating that keeps them suspended better while baking!
