Made with vanilla protein powder and almond flour, these pumpkin protein muffins are a delicious grain-free baked good that’s perfect for breakfast or as a snack.
The pumpkin adds flavor and moisture, while the melted bits of dark chocolate chips make them taste like a treat. You might want to double the recipe because your family will love these healthy muffins.

This blog post is sponsored by Bob’s Red Mill. All opinions are my own.
The best part is that they come together quickly in a bowl as you can see in this video.
High Protein Muffin Recipe
If you love a good muffin for breakfast but want a more nutritious recipe, these pumpkin muffins are a great option. Made with almond flour and protein powder, each muffin packs 5 grams of protein, has a great texture and an irresistible pumpkin-vanilla flavor.
Enjoy one of these muffins with Greek yogurt or scrambled eggs and fruit to make it a balanced meal of carbs, healthy fats, and protein, so you are satiated and full of energy for hours.
Ingredients for Pumpkin Protein Muffins
- Bob’s Red Mill Vanilla Protein: I love this option but you can use ¾th cup of any vanilla protein powder.
- baking powder: a leavening agent that gives to help these muffins rise.
- almond flour: a grain-free flour that’s made from finely ground almonds. Its high-fat content and texture make baked goods soft and moist.
- eggs: are a binding agent that holds the ingredients together and helps the muffins rise.
- honey: just ¼ cup is all you need to give these healthy muffins the right amount of sweetness.
- pumpkin purée: instead of butter, we use pumpkin puree for a healthier alternative and delicious pumpkin flavor.
- milk: any kind will do. I like to use unsweetened almond milk.
- chocolate chips: optional, but the taste of dark chocolate chips in a freshly baked muffin is irresistible.

How to Make Pumpkin Protein Muffins
Grab a large mixing bowl and let’s make these healthy muffins!
- Make the batter
Combine the vanilla protein, baking powder, and almond flour in a large bowl. Add the eggs, honey, pumpkin, and milk. Mix the ingredients to form a thick batter. - Add some chocolate
Fold in the chocolate chips and divide the batter between 8 muffin cups. - Bake to perfection
Place the muffins into the oven and bake for 22-25 minutes or until a toothpick comes out clean when inserted in the center of a muffin. - Let them cool off
Remove the pan from the oven and allow the muffins to cool slightly before serving. - In case of leftovers
Refrigerate the last few muffins in an airtight container for up to a week.
Along with their delicious pumpkin flavor, the best part is that they come together so easily, as you can see in this video:
Best Protein Powder for Muffins
If you want to make protein muffins, it’s a good idea to start with a high-quality protein powder that DOES NOT contain whey.
While whey protein powder is great for smoothies, it can make baked goods turn out tough and rubbery. Instead, I like to use plant-based options such as pea protein, and Bob’s Red Mill Vanilla Protein Powder is a an excellent choice.
It’s made with pea protein, includes probiotics, and is sweetened with monk fruit, so we don’t have to worry about added sugars or artificial ingredients.

Ingredient Swaps for Pumpkin Protein Muffins
Below are a few ingredient swaps you can implement into this recipe and still achieve delicious results.
Swap almond flour for oat flour
If you need a nut-free version and still want to keep the recipe gluten-free, use oat flour instead. You can make your own oat flour or purchase it from Bob’s Red Mill.
Swap almond butter for a nut-free alternative.
Sunflower butter or tahini butter are both great alternatives for almond butter.
Swap mashed banana for canned pumpkin
Replace the pumpkin puree with equal parts mashed banana or unsweetened applesauce. The muffins will still have a soft and moist texture.

More Recipes with Protein Powder
I’m always looking for ways to add more protein into my family’s day, and protein powder makes it easy to do! Below are more recipes made with protein powder that have received the ‘thumbs up’ from my family.
- Breakfast Cookies
- Stovetop Protein Oatmeal
- High Fiber and Protein Chocolate Smoothie Bowl
- Protein Pancakes (no banana!)

Pumpkin Protein Muffins with Chocolate Chips
Ingredients
- ¾ cup Bob’s Red Mill Vanilla Protein
- 1 tablespoon baking powder
- 1 cup almond flour
- 2 large eggs, whisked
- ¼ cup honey
- 1 cup pumpkin
- ¾ cup milk, any kind
- ⅓ cup chocolate chips
Instructions
- Preheat the oven to 350F. Lightly grease or line an 8-count muffin tin with cooking spray or paper liners.
- In a large mixing bowl, combine the vanilla protein, baking powder, and almond flour. Add the eggs, honey, pumpkin, and water, and mix to form a thick batter. Fold in the chocolate chips.
- Divide the batter among the muffin cups, filling them ¾th of the way, and bake for 22-25 minutes or until a toothpick inserted in the center of a muffin comes out clean.
- Remove the pan from the oven and allow the muffins to cool slightly before serving.
- Store extras in an airtight container in the refrigerator for up to a week.
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