Craving pumpkin goodies? These Protein Pumpkin Muffins are a healthy option!
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‘Tis the season for all things pumpkin! Let’s make pumpkin protein muffins that are healthy, delicious, and have a higher protein content than your average muffin.
Recipe Ingredients–What You Need
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Melted butter: Adds moisture and rich flavor so each muffin is deliciously tender.
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Coconut sugar: Coconut sugar adds a deep flavor to these muffins and is less refined than regular white sugar or brown sugar.
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Vanilla extract: Infuses the muffins with a warm flavor that compliments the pumpkin perfectly.
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Greek Yogurt: Greek yogurt is what boosts the protein content without protein powder. I use whole milk Greek yogurt, but you can also use cottage cheese here like I do in my Cottage Cheese Blueberry Muffins.
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Whole milk: Whole milk is for creaminess and helps create a smooth batter.
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Pumpkin Puree: I use canned pumpkin and I recommend organic pumpkin if it’s available.
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Whole eggs: Eggs bind the dry and wet ingredients together and also give us the perfect texture.
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All-purpose flour: I use AP flour for the foundation of the muffins and to provide the necessary structure. If you need these to be gluten free, use an all-purpose gluten-free flour. You can also sub in half whole wheat flour or use all whole wheat pastry flour.
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Rolled oats: Rolled oats add a boost of fiber, more protein, as well as manganese, magnesium, phosphorus, iron, zinc, and B vitamins to these muffins.
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Ground flaxseed meal: Adding flaxseed to my baking is one of my favorite ways to boost the nutrition!
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Baking soda: As a leavening agent.
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Salt: Salt brings out all the flavors of your ingredients.
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Pumpkin Pie Spice: When you’re craving something “pumpkin flavored,” this is the spice blend you’re craving! If you don’t have any on hand, make my Homemade Pumpkin Pie Spice Mix.
- Cinnamon: I add a little extra cinnamon for the warm seasoning it brings.
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Optional add ins or toppings: You can add chocolate chips or white chocolate chips to the batter, or top with pumpkin seeds for a little crunch and a boost of magnesium!
Step-By-Step Instructions for Pumpkin Protein Muffins 
- Preheat the oven to 400 degrees. Line your muffin tins with paper or silicone liners and set aside.

- In a medium bowl, whisk together the melted butter, coconut sugar, and vanilla.

- When it is combined, add the Greek yogurt, milk, pumpkin, and eggs. Whisk until combined.

- To the same bowl, add all of the dry ingredients: the flour, rolled oats, flaxseed meal, baking soda, salt, pumpkin pie spice, and cinnamon. Stir with a wooden spoon until just combined.

- Transfer the batter to the prepared muffin tin, filling each cup totally full.

- Bake in the 400 degree oven for 5 minutes, then turn the tray 180 degrees and reduce the heat to 350 degrees. Bake for an additional 12-15 minutes, until a toothpick inserted into the center of a muffin does not come out with raw batter on it. Allow to cool on a baking rack before removing muffins from tin. Enjoy!

I hope you love these Pumpkin Protein Muffins as much as we do! If you try it, or any of my other healthy recipes, please comment and give a star rating below. It’s really helpful for readers to see which recipes are tried and true! I appreciate you. Follow along on Instagramand Facebook, too.
Pumpkin Protein Muffins
- Total Time: 35 minutes
- Yield: 12 muffins 1x
Ingredients
- 6 tablespoons butter, melted
- 3/4 cup coconut sugar
- 1/2 teaspoon vanilla extract
- 1 1/2 cups Greek yogurt
- 1/3 cup whole milk
- 1/2 cup pumpkin puree
- 2 eggs
- 1 3/4 cup AP flour
- 1/2 cup ground flaxseed meal
- 1/2 cup rolled oats
- 1/2 teaspoon salt
- 1 1/2 teaspoons baking soda
- 2 teaspoons pumpkin pie spice mix
- 1/2 teaspoon cinnamon
Instructions
- Preheat the oven to 400 degrees. Line your muffin tins with paper or silicone liners and set aside.
- In a medium bowl, whisk together the melted butter, coconut sugar, and vanilla. When it is combined, add the Greek yogurt, milk, pumpkin, and eggs. Whisk until combined.
- To the same bowl, add all of the dry ingredients: the flour, rolled oats, flaxseed meal, baking soda, salt, pumpkin pie spice, and cinnamon. Stir with a wooden spoon until just combined.
- Transfer the batter to the prepared muffin tin, filling each cup totally full.
- Bake in the 400 degree oven for 5 minutes, then turn the tray 180 degrees and reduce the heat to 350 degrees. Bake for an additional 12-15 minutes, until a toothpick inserted into the center of a muffin does not come out with raw batter on it. Allow to cool on a baking rack before removing muffins from tin. Enjoy!
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Category: muffin recipes
- Method: baking
- Cuisine: American
Nutrition
- Serving Size: 1 muffin
- Calories: 254
- Sugar: 14.2 grams
- Fat: 8.6 grams
- Saturated Fat: 4.8 grams
- Trans Fat: 0 grams
- Carbohydrates: 31.2 grams
- Fiber: 2.7 grams
- Protein: 8.1 grams








All-purpose flour: I use AP flour for the foundation of the muffins and to provide the necessary structure.
Baking soda is in the write-up, but not in the recipe. How much should I add? Looking to make these today. Thank you!
Than you for the heads up! It should call for 1 1/2 teaspoons of baking soda. Fixing the recipe card now!