September and October will forever be my favorite months. The cooler mornings, changing leaves, cozy sweaters, football, and pumpkin everything. I wish I could bottle up this time of year and keep it around forever! And once September hits, pumpkin muffins are an absolute must.

These High-Protein Pumpkin Cream Cheese Muffins are my take on the classic coffee-shop pumpkin cream cheese muffin, but with a little Bridgette upgrade. They’re soft and pumpkin-y, filled with warm fall spices, have that creamy center we all want, and I’ve added protein powder to make them a little more satisfying.

They’re perfect with coffee in the morning, as an afternoon snack, or honestly straight out of the fridge when you remember they’re sitting in there.

Why You’ll Love These

Traditional pumpkin muffins are delicious, but I wanted these to have a little more staying power. The combination of oat flour, almond flour, eggs and protein powder adds protein while pumpkin and applesauce help keep them soft and moist.

And then there’s the cream cheese center. Don’t skip it! That creamy, slightly sweet filling against the spiced pumpkin muffin is what makes these SO good.

The Question I always Get Asked

One of the questions I get the most often is: “What kind of protein powder so you use in your recipes?” I always use Momentous because it’s genuinely one of my favorite protein powders. I use it all the time, not just in shakes, but in oatmeal, baked goods and recipes like this when I want an easy way to add a little more protein.

One thing to remember when baking with protein powder: different formulas absorb liquid differently, so swapping brands can slightly change the final texture.

Want to try the one I use? You can grab it here and use my link for 15% off:
My favorite protein powder

Affiliate disclosure: This post contains affiliate links, which means I may earn a commission if you purchase through my link, at no additional cost to you.

High-Protein Pumpkin Cream Cheese Muffins

Makes: approximately 10–12 muffins
Prep time: 15 minutes
Bake time: 24–28 minutes
Oven: 350°F

Dry Ingredients

• ¾ cup oat flour
• ¾ cup almond flour
• ½ cup vanilla protein powder (I use this one)
• 1 teaspoon cinnamon
• ½ teaspoon pumpkin pie spice
• 1½ teaspoons baking powder
• ½ teaspoon salt

Wet Ingredients

• 2 large eggs
• ¾ cup pumpkin purée
• ¼ cup unsweetened applesauce
• ¼ cup pure maple syrup
• ¼ cup plant-based milk
• 1 teaspoon vanilla extract

Maple Cream Cheese Filling

• 4 ounces cream cheese, softened
• ¼ cup plain Greek yogurt
• 2 tablespoons pure maple syrup
• ½ teaspoon vanilla extract
• Pinch of cinnamon or pumpkin pie spice

Optional Topping

• Pumpkin seeds/pepitas
• Sprinkle of cinnamon or pumpkin pie spice

Instructions

1. Preheat the oven to 350°F. Lightly grease a muffin pan or line it with muffin liners.
2. In a large bowl, whisk together the oat flour, almond flour, protein powder, cinnamon, pumpkin pie spice, baking powder and salt.
3. In a separate bowl, whisk the eggs, pumpkin purée, applesauce, maple syrup, plant-based milk and vanilla until smooth.
4. Pour the wet mixture into the dry ingredients and gently stir until just combined. Avoid overmixing. The batter should be thick and scoopable rather than runny.
5. For the filling, beat the softened cream cheese, Greek yogurt, maple syrup, vanilla and cinnamon until smooth and creamy.
6. Divide the pumpkin batter among the muffin cups. Pipe or spoon approximately 2 teaspoons of cream cheese filling into the center of each muffin, gently pressing most of the filling into the batter while leaving a little visible on top.
7. Sprinkle with pepitas, if desired.
8. Bake for 24–28 minutes, or until the tops appear set and a toothpick inserted into the pumpkin portion of the muffin (not directly through the cream cheese) comes out with a few moist crumbs rather than wet batter.

This part is important: allow the muffins to cool in the pan for at least 20–30 minutes before removing them. Because these are very moist and have a cream cheese center, they’ll be much more delicate while they’re hot and will firm considerably as they cool.

For the best texture, let them cool completely before breaking one open.

Storage

Because of the cream cheese filling, store leftover muffins covered in the refrigerator. I actually love them chilled, but you can also let one sit at room temperature for a few minutes before eating.

A Dietitian’s Take

I just love finding simple ways to make the foods we already enjoy a little more satisfying. Pair one with a latte, Greek yogurt, eggs, or another protein source and you’ve got a much more substantial fall breakfast or snack.

Because eating for performance doesn’t mean skipping the pumpkin muffin. It means learning how to build meals and snacks that support your goals and include foods you genuinely love. And in September and October? The pumpkin muffin is staying.