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Pumpkin Protein Muffins (Moist, Oat Flour, 12g Protein Each)

By Ami·September 27, 2026·★★★★★4.8 from 58 votes·Jump to RecipePrint

Pumpkin protein muffins were my fall project this year, because every protein muffin I had eaten was either dry as a sponge or tasted like the inside of a protein tub — these are moist, domed, warmly spiced pumpkin chocolate chip muffins with 12 grams of protein each, made with oat flour, vanilla protein powder and Greek yogurt.

It took me seven batches. The breakthroughs were Greek yogurt instead of oil for moisture, a whey-casein blend instead of pure whey (pure whey bakes rubbery), and pulling them from the oven a couple of minutes before they look done. They are built exactly like my blueberry protein muffins, just with a full cup of pumpkin and a lot more cinnamon.

Pumpkin protein muffins, domed and golden-orange in paper liners, topped with chocolate chips and pumpkin seeds, one split open to show a moist crumb
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Why these pumpkin protein muffins stay moist.

Here's what you'll need.

Pumpkin puree, plain Greek yogurt, eggs, maple syrup, vanilla, a little melted coconut oil, oat flour, vanilla protein powder (a whey-casein blend bakes best), pumpkin pie spice, baking soda, baking powder, salt, mini chocolate chips, and pumpkin seeds for the tops.

Ingredients for pumpkin protein muffins in small bowls: pumpkin puree, Greek yogurt, eggs, maple syrup, vanilla, oat flour, vanilla protein powder, pumpkin pie spice, baking soda, chocolate chips and pumpkin seeds for healthy pumpkin muffins

Here's how it all comes together.

STEP 1 — WHISK THE PUMPKIN MIXTURE

Heat the oven to 350°F and line a 12-cup muffin tin with paper liners (spray the liners lightly; protein muffins love to stick to paper). In a large bowl, whisk the pumpkin, Greek yogurt, eggs, maple syrup, melted coconut oil and vanilla until completely smooth and glossy.

Pumpkin puree, Greek yogurt, eggs, maple syrup and vanilla being whisked together in a large bowl
STEP 2 — COMBINE THE DRY INGREDIENTS

In a separate bowl, whisk the oat flour, protein powder, pumpkin pie spice, baking soda, baking powder and salt. Break up any clumps of protein powder with the whisk — those clumps turn into chalky pockets in the baked muffins if you leave them.

Oat flour, vanilla protein powder, pumpkin pie spice and baking soda whisked together in a bowl
STEP 3 — FOLD, DO NOT BEAT

Add the dry ingredients to the pumpkin mixture and fold with a spatula just until no dry streaks remain. The batter will be thick, closer to a soft cookie dough than a pancake batter. Stop as soon as it comes together; overmixing a protein batter is what makes muffins tough and tunneled.

The dry oat flour and protein powder mixture being folded into the orange pumpkin batter with a spatula
STEP 4 — STIR IN THE CHOCOLATE CHIPS

Fold in most of the mini chocolate chips, saving a tablespoon for the tops. Mini chips distribute better than regular ones in a thick batter and do not sink. Let the batter sit for 5 minutes while you get the tin ready; the oat flour hydrates and the muffins dome higher.

Mini chocolate chips being stirred into thick pumpkin protein muffin batter in a bowl
STEP 5 — SCOOP INTO THE TIN

Divide the batter among the 12 cups with a large cookie scoop, filling each one right to the top. That full scoop is what gives you a real domed muffin instead of a flat one. Scatter the reserved chocolate chips and the pumpkin seeds over the tops and press them in gently.

Thick pumpkin chocolate chip batter being scooped into a paper-lined muffin tin
STEP 6 — BAKE AND COOL ON A RACK

Bake for 18 to 20 minutes, until the tops are domed and spring back when pressed and a toothpick in the center comes out with a few moist crumbs. Do not wait for a perfectly clean toothpick; protein muffins dry out fast in the last two minutes. Cool 5 minutes in the tin, then move them to a rack.

Baked pumpkin protein muffins, domed and golden with chocolate chips and pumpkin seeds on top, cooling on a wire rack
Two pumpkin protein muffins on a cream plate, one split open to show the moist orange crumb and melted chocolate chips, with a mug of coffee and a small pumpkin behind
GLP-1 High Protein High Fiber Cookbook coverIf you want more breakfasts and snacks built this way — protein and fiber first, easy to portion, satisfying on a smaller appetite — this is the book I bake from, the Ultimate GLP-1 High Protein High Fiber Cookbook.

Things I learned while testing this recipe.

Why pumpkin protein muffins are my weekday breakfast this fall.

Here's what I'd serve with this.

Just in case you have leftovers.

Storing: Cool the muffins completely, then store them in an airtight container at room temperature for 2 days or in the fridge for up to 5 days (put a paper towel in the container to catch moisture). To freeze, put them in a freezer bag for up to 3 months.

Reheating: Microwave a refrigerated muffin for 15 to 20 seconds; from frozen, 35 to 45 seconds. For a crisp top, 3 minutes in the air fryer or toaster oven at 325°F. Split it and add a thin swipe of nut butter while it is warm.

More easy breakfast recipes...

Blueberry protein muffinsBlueberry protein muffins High protein banana baked oatmealHigh protein banana baked oatmeal Greek yogurt banana breadGreek yogurt banana bread Cottage cheese protein pancakesCottage cheese protein pancakes

If you like a sweet breakfast with protein built in, my fudgy protein brownies use the same yogurt-for-oil swap. And today's other new pumpkin recipes are my pumpkin baked oatmeal and pumpkin bars with cream cheese frosting for dessert.

Pumpkin Protein Muffins

Moist pumpkin protein muffins made with oat flour, vanilla protein powder, Greek yogurt and pumpkin puree, with chocolate chips and pumpkin seeds on top. 30 minutes, about 185 calories and 12g protein each.

Prep10 min
Cook20 min
Total30 min
Servings12 muffins
CategoryBreakfast · Quick Breakfasts
CuisineAmerican

Ingredients

Instructions

  1. Prep: Heat the oven to 350°F. Line a 12-cup muffin tin with paper liners and spray them lightly.
  2. Wet: Whisk the pumpkin, Greek yogurt, eggs, maple syrup, coconut oil and vanilla until smooth.
  3. Dry: In another bowl, whisk the oat flour, protein powder, pumpkin pie spice, baking soda, baking powder and salt.
  4. Fold: Fold the dry ingredients into the wet just until combined, then fold in all but 1 tablespoon of the chocolate chips. Rest the batter 5 minutes.
  5. Scoop: Divide among the 12 cups, filling them to the top. Sprinkle with the remaining chocolate chips and the pumpkin seeds.
  6. Bake: Bake 18–20 minutes, until domed and a toothpick shows a few moist crumbs. Cool 5 minutes in the tin, then on a rack.

Notes

A whey-casein blend protein powder gives the softest muffins; with pure whey, use ½ cup and add ¼ cup more oat flour. Make oat flour by blending rolled oats until fine. Do not overbake — protein muffins dry out quickly. Swap the chocolate chips for chopped walnuts or dried cranberries. Nutrition is per muffin and will vary with the protein powder you use.

Nutrition (per serving, estimate): 185 calories · 12g protein · 21g carbs · 7g fat · 3g fiber · 215mg sodium
GLP-1 High Protein High Fiber Cookbook cover

High protein, high fiber, and built for a GLP-1 appetite.

The Ultimate GLP-1 High Protein High Fiber Cookbook is full of breakfasts and snacks like these muffins — small, satisfying and heavy on protein and fiber, for the days you need to eat well without eating a lot.

Get the cookbook on Amazon
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Pumpkin protein muffins FAQ

Why are my protein muffins dry or rubbery?

Usually one of three things: pure whey protein (it bakes rubbery), too much flour or protein powder, or overbaking. Use a whey-casein blend, measure the oat flour by weight, and pull the muffins when a toothpick still shows a few moist crumbs.

What protein powder is best for pumpkin protein muffins?

A whey-casein blend gives the softest, moistest texture. Pure whey works if you reduce it to ½ cup and add a little more oat flour. Plant proteins absorb more liquid, so add 2 to 3 tablespoons of milk to the batter if you use one.

Can I make these pumpkin muffins without protein powder?

Yes. Replace the protein powder with ¾ cup more oat flour. They will be lighter and more like a classic healthy pumpkin muffin, with about 6g of protein each instead of 12g.

How much protein is in each pumpkin protein muffin?

About 12g per muffin with 3 scoops of vanilla protein powder, Greek yogurt and 3 eggs, at around 185 calories. The exact number depends on your protein powder, so check its label.

Can you freeze pumpkin protein muffins?

Yes, they freeze very well. Cool them completely, then freeze in a zip-top bag for up to 3 months. Microwave a frozen muffin for 35 to 45 seconds, or let it thaw on the counter for an hour.