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These moist and delicious pumpkin protein muffins are made with pumpkin puree, greek yogurt, eggs, almond flour, protein powder, cinnamon, and maple syrup. You can make them in no time and enjoy them all week long as a healthy treat or quick breakfast. They are gluten-free, low in carbs, and refined sugar-free!

I am here for all things pumpkin this time of year and these pumpkin protein muffins are my new favorite treat! I have also been making pumpkin cookies and pumpkin donuts on repeat, so muffins were the logical next thing to bake!
These pumpkin muffins are packed with protein, fiber, and vitamins, are super moist and flavorful, and only require a few simple ingredients that you probably already have.
Why you’ll love these pumpkin protein muffins
- They are made with a few simple, healthy ingredients.
- Gluten-free low-carb, and refined sugar-free!
- Super easy to make in only a few simple steps.
- Great for meal prep!
- They make a wonderful protein-packed healthy snack, sweet treat, or breakfast!

How much protein is in Protein Muffins?
These muffins pack about 11 grams of protein per muffin! Where does the protein come from?
- Greek yogurt
- Protein powder
- Eggs
- Almond flour
How great is that? They also only have 159 calories per muffin, plus fiber, vitamin C, calcium, and healthy fat. These really are incredible muffins. Perfect for fall and really any time of year!
Ingredients You Will Need

- Pumpkin puree – make sure it is not pumpkin pie filling.
- Greek yogurt – plain greek yogurt. I used the Chobani brand.
- Almond flour – blanched almond flour. I used Bob’s Red Mill brand.
- Vanilla protein powder – I used a plant-based protein powder but whey protein powder also works.
- Eggs – two large eggs
- Maple syrup – just a little bit to add some sweetness to the muffins.
- Vanilla extract
- Warm spices – ground cinnamon and pumpkin pie spice.
- Baking powder
- Chocolate chips – I like to use dark chocolate chips. You can use mini or regular-size chocolate chips.
- Salt – used to enhance all of the flavors.
How to make Healthy Pumpkin Protein Muffins
- Combine the almond flour, protein powder, baking powder, cinnamon, pumpkin pie spice, and salt in a medium-size mixing bowl.
- Add the wet ingredients (pumpkin puree, greek yogurt, eggs, vanilla, maple syrup) to a high-speed blender or food processor and blend.
- Pour blended wet ingredients into a mixing bowl with the dry ingredients and stir to combine into a thick muffin batter.
- Then fold in the chocolate chips.
- Divide the batter between 12 lined muffin cups, and bake in a 350-degree F oven for 30-35 minutes, until the tops are nice and golden brown and firm.
- Remove, let cool for at least 25-30 minutes and serve with some almond butter.








So simple, but super delicious!!!!
Recipe Tips
- To keep the fat down, use nonfat plain greek yogurt. Regular greek yogurt also works.
- Use real pumpkin puree, not pumpkin pie filling.
- To keep the sugar low in this recipe, I used mini sugar-free dark chocolate chips, Lilys brand.
- Use blanched almond flour and not just pulsed almonds. It literally makes all of the difference. Oat flour also works in this recipe in the same amount as almond flour.
- You can use plain or vanilla protein powder. I have not tried this with chocolate protein powder but I am sure that would also be delicious.
- Let the muffins cool completely (at least 30 minutes) before eating. These muffins will be very soft on the inside after they bake, which is why they need the cooling time. This will allow the center to condense and get nice and firm and fluffy but still moist and delicious.
- To make these protein muffins vegan, you can use vegan protein powder, diary free greek yogurt, and flax egg.

What is the best protein powder to use for muffins?
I have tried a few different protein powders. Here are the ones that I found worked best in this muffin recipe.
- KOS Vanilla Protein Powder
- Alkamind Vanillla Protein Powder
- Orgain Protein Powder
- Clean, Simple Eats – Whey Protein Powder
How to store protein muffins
You can easily store these pumpkin protein muffins in an airtight container and keep in a cool, dry place (aka back of kitchen counter or pantry) for up to 4 days, although they didn’t last that long in my house.
Can I freeze these pumpkin muffins?
I do not recommend freezing pumpkin protein muffins since they are best if eaten within a few days of making them.

More healthy muffin recipes
- Gluten-Free Cranberry Orange Muffins
- Best Healthy Zucchini Muffins –
- Double Chocolate Zucchini Muffins – Gluten Free
- Healthy Apple Muffins
- Gluten Free Chocolate Chip Muffins
Other protein packed treats to try!
- Protien Cookie Dough Bites
- Cherry Banana Smoothie
- Healthy Chocolate Protein Shake
- Almond Flour Chocolate Chip Blondies
Did you make this pumpkin protein muffins recipe? If you did, then please leave a rating and comment below. You can also tag me on Instagram @pinchmegoodfood so I can see your creation.
Print
Healthy Pumpkin Protein Muffins
- Total Time: 40 minutes
- Yield: 12 people 1x
- Diet: Gluten Free
Description
Protein-packed, super moist, and delicious! These Pumpkin Protein Muffins are the perfect mid-afternoon or pre-workout snack to energize you and satisfy that sweet tooth! Gluten-free, refined sugar-free, and refined flour free!
Ingredients
- 1.5 cups blanched almond flour
- 4 tablespoons vanilla protein powder
- 1.5 teaspoons pumpkin pie spice
- 1 teaspoon ground cinnamon
- 1 teaspoon baking powder
- 1/4 teaspoon kosher salt
- 1 cup pumpkin puree (not pumpkin pie filling)
- 1 cup plain greek yogurt
- 2 large eggs, lightly whisked
- 1 tablespoon maple syrup (plus 1 teaspoon )
- 1 teaspoon vanilla extract
- 3/4 cup mini or regular chocolate chips
Instructions
- Preheat oven to 350 degrees F and line a 12-cup muffin pan with muffin liners and lightly spray them with cooking spray.
- In a medium-sized mixing bowl combine the almond flour, protein powder, pumpkin pie spice, cinnamon, baking powder, and salt.
- Add all of the pumpkin puree, greek yogurt, eggs, maple syrup, and vanilla to a high-speed blender and pulse to combine.
- Pour the blended wet ingredients into the mixing bowl with the dry ingredients, and mix until a smooth batter forms.
- Fold in 2/3 cup of the chocolate chips into the batter – I used mini chocolate chips.
- Evenly divide the batter between the muffin cups, filling each about ¾ full. Top each with the remaining chocolate chips. Tip: about 1/4 cup of batter in each muffin cavity was a good amount.
- Bake in the middle rack of your preheated oven for 30-35 minutes, until the tops are nice and golden brown.
- Remove from the oven, let cool for at least 30 minutes, and enjoy!
Notes
- Use blanched almond flour and not just pulsed almonds. It literally makes all of the difference. Oat flour also works in this recipe in the same amount as almond flour.
- You can use plain or vanilla protein powder. I have not tried this with chocolate protein powder but I am sure that would also be delicious.
- Let the muffins cool completely (at least 30 minutes) before eating since they will stick to the muffin liners if they do not cool enough.
- These muffins can be stored for up to 4 days in an airtight container.
- For even size muffins use an ice cream scoop to fill the muffin cups with the batter.
- Prep Time: 5 minutes
- Cook Time: 35 minutes
- Category: Breakfast
- Method: Baking
- Cuisine: American
Keywords: pumpkin protein muffins, pumpkin muffins, protein muffins, muffins.
YUM!
I made these for my preworkout snack and they are so good! I see that you write near the top that there are 77 calories per muffin, but in your nutrition info you list 159 calories per muffin. My calorie calculator says each muffin has 190 calories (but I also used full fat home made Greek yogurt).
Agree. This was disappointing.
The nutritional information is only an estimate based on the calorie calculator that I use. This information can change based on the size of the muffins and the brand/type of ingredients. I will update the post so it reflects the same amount of calorie noted in my recipe card. Thank you for making me aware of the discrepancy. I hope you still enjoyed them!