Pumpkin Protein Muffins (Healthy!)

These healthy pumpkin protein muffins are fluffy, moist, and full of cozy fall flavors with over 9 grams of protein each. Made with almond flour, Greek yogurt, and protein powder, they're naturally gluten-free and easy to whip up in one bowl — perfect for a quick breakfast, snack, or meal prep in under 30 minutes.

Healthy chocolate chip pumpkin protein muffins with super fluffy, moist center.

A Quick Look At The Recipe

✅ Recipe Name: Healthy Pumpkin Protein Muffins
🕒 Ready In: 25 minutes
👪 Serves: 12 muffins
🍽 Calories: ~196 calories per muffin
💪 Protein: ~9g per muffin
🥣 Main Ingredients: Almond flour, pumpkin purée, Greek yogurt, protein powder, eggs, maple syrup
📖 Dietary Info: High protein, gluten-free, naturally sweetened, healthy, vegetarian
⭐ Why You'll Love It: Moist, fluffy, and full of warm pumpkin spice. Made with almond flour and protein powder for a naturally gluten-free, high-protein muffin that's perfect for fall.

SUMMARIZE & SAVE THIS CONTENT ON

These pumpkin protein muffins are my fall favorite because they strike the perfect balance — soft, fluffy, and full of cozy spice while still packing a good boost of protein (just like these healthy protein powder banana muffins). I love that they're naturally gluten-free thanks to almond flour and stay super moist from Greek yogurt (no dry, crumbly muffins here!).

They're also so versatile — perfect for breakfast with coffee, an afternoon snack, or tucked into meal prep for the week. I make them on repeat all season long, right alongside my Healthy Pumpkin Bread and Pumpkin Oatmeal Bars.

Jump to:

A Quick Look At The Recipe
Why You'll Love This Recipe
Ingredients You'll Need
Easy Substitutions & Variations
Need to substitute an ingredient?
How to Make Pumpkin Protein Muffins
1 Minute Video Tutorial
Expert Tips
Troubleshooting Pumpkin Protein Muffins
Frequently Asked Questions
Storage, Freezing & Reheating
More Healthy Pumpkin Recipes You'll Love
📖 Recipe
💬 Comments

Why You'll Love This Recipe

Protein-Packed: Each pumpkin muffin has about 9 grams of protein (can increase with a higher-protein powder). Just like my pumpkin protein pancakes!
Wholesome Ingredients: Made with almond flour, Greek yogurt, pumpkin purée, and protein powder.
Quick & Easy: One bowl, 25 minutes, and they're ready to enjoy.
Great for Meal Prep: Bake once and have healthy snacks all week.
Naturally Sweetened: Lightly sweetened with coconut sugar and maple syrup.
Gluten-Free: Made with almond flour and naturally gluten-free ingredients.
Cozy Fall Flavor: Warm pumpkin spice and cinnamon make every bite taste like fall.

⭐⭐⭐⭐⭐

These were really good. I liked how moist they were and that they had so much protein in them. Also, a plus that it was gluten-free.

- Janet

Ingredients You'll Need

All the ingredients for pumpkin protein muffins in small bowls, each with labels including almond flour, pumpkin purée, Greek yogurt, protein powder, eggs, maple syrup, almond butter, and spices.

Pumpkin purée: The star of these muffins. It keeps them moist, adds natural sweetness, and gives that classic pumpkin flavor. Always choose pure pumpkin purée, not pie filling.
Almond butter: Adds healthy fats and also helps bind the batter for a soft, tender crumb. Use creamy, unsweetened almond butter for the best texture.
Greek yogurt: Boosts protein and ensures the muffins stay moist without needing oil. A 2% or whole milk yogurt gives a richer texture, while nonfat or dairy-free options also work.
Eggs: Provide structure and help the muffins rise so they're fluffy instead of dense.
Protein powder: The key to making these true pumpkin protein muffins. Whey protein creates a softer, cake-like muffin, while plant-based protein works too, just with a slightly denser texture.
Almond flour: Skip almond meal — it's coarse and can make the muffins grainy. Super-fine almond flour works best.
Pumpkin pie spice + cinnamon: Bring warm, cozy flavors to every bite. If you don't have pumpkin pie spice, you can make your own with cinnamon, nutmeg, ginger, and cloves.
Maple syrup + coconut sugar: Natural sweeteners that add depth of flavor without refined sugar. Maple syrup keeps the muffins moist, while coconut sugar adds a caramel-like sweetness.
Milk: Helps thin the batter so it mixes easily. Any milk—dairy or non-dairy—works well.
Baking powder: Essential for lift and fluffiness in each muffin.

Scroll to the recipe card at the bottom of this page for exact quantities.

Easy Substitutions & Variations

Dairy-free option: Replace Greek yogurt with a thick dairy-free yogurt (like coconut or almond milk yogurt) and use plant-based protein powder.
Nut-free option: Use sunflower seed butter instead of almond butter and swap almond flour for oat flour. (Note: sunflower butter may turn the muffins slightly green from a natural reaction — totally safe and tasty!).
Mini muffins: Bake in a mini muffin tin for about 10–12 minutes — perfect for lunchboxes or quick snacks.
Protein Powder: Play around with your favorite flavors — vanilla, pumpkin spice, coffee, or even snickerdoodle all work well.
Almond Flour: This recipe is designed for almond flour, so the muffins stay moist and fluffy. If you want to bake with another flour, check out my oat flour pumpkin muffins and these healthy banana pumpkin muffins.
Sweeteners: Coconut sugar can be swapped with light brown sugar, and maple syrup can be swapped with honey.
Add mix-ins: Fold in chopped pecans, walnuts, or pumpkin seeds for a crunchy bite.

Super moist and fluffy healthy, high protein pumpkin muffins with chocolate chips.

Need to substitute an ingredient?

Ask AI for suggestions on how to substitute the particular ingredient.

How to Make Pumpkin Protein Muffins

All the wet ingredients for pumpkin protein muffins whisked together in a large mixing bowl until smooth.

Step 1: In a large bowl, whisk together the eggs, pumpkin purée, Greek yogurt, almond milk, maple syrup, and coconut sugar until smooth.

Protein powder, almond flour, and chocolate chips being added to the pumpkin muffin batter in a mixing bowl.

Step 2: Add the almond flour, protein powder, pumpkin spice, cinnamon, and baking powder. Gently fold until just combined, then stir in chocolate chips if using.

Unbaked pumpkin protein muffin batter divided into a cupcake tin, topped with chocolate chips before baking.

Step 3: Divide the batter evenly between muffin cups, filling each about two-thirds full. Sprinkle extra chocolate chips on top for a bakery-style finish.

Freshly baked pumpkin protein muffins in a cupcake tin, golden and topped with chocolate chips.

Step 4: Bake at 350°F for 18–20 minutes, or until a toothpick comes out clean. Let the muffins cool before removing the liners and serving.

1 Minute Video Tutorial

Expert Tips

Use a quality protein powder. Whey protein gives the fluffiest, cake-like texture. If you're using plant-based powder, just know the muffins will be a little denser (still super tasty!).
Use pure pumpkin purée. Skip pumpkin pie filling. Brands vary — I tested a few, and found that Farmer's Market Organic Pumpkin Purée always gives the most consistent texture. Libby's also works well if you prefer a thicker purée.
Don't overmix. Once the dry ingredients are in, gently stir until just combined. Overmixing is the fastest way to end up with dense muffins.
Watch the bake time. These muffins cook quickly. Check at 15 minutes to keep them moist and prevent drying out.

Troubleshooting Pumpkin Protein Muffins

My muffins turned out dry. This usually means they were overbaked or too much protein powder was used. Check them a few minutes early and use a kitchen scale for accuracy.
They sank in the middle. That's often from underbaking or not letting them cool properly. Make sure a toothpick comes out clean, and let them set in the pan before peeling off the liners.
The muffins are dense or gummy. Overmixing the batter can knock out air and create dense muffins. Stir gently until the dry ingredients are just combined.
They're sticking to the liners. Almond flour batters can be clingy. Use parchment-style liners or lightly spray your pan for easy release. Also, make sure they are completely cool before pulling out of the liners.
Not sweet enough for me. Everyone's taste is different! Add a few extra tablespoons of coconut sugar or stir in chocolate chips for more sweetness.

Super moist pumpkin protein muffins with mini chocolate chips.

Frequently Asked Questions

What's the best protein powder for baking?

I like to use vanilla whey protein powder for the fluffiest muffins, but pea protein works well, too! For the best results, choose a plain or vanilla-flavored protein powder.

Why did my pumpkin protein muffins turn out dry?

They were probably overbaked or had too much protein powder. Check them a few minutes early and measure with a kitchen scale for accuracy.

Can I use fresh pumpkin instead of canned pumpkin purée?

Yes, you can use fresh pumpkin purée. Just cook and purée a small pumpkin or butternut squash, then drain it well to achieve the right consistency before using it in your recipe.

Can I use cottage cheese instead of Greek yogurt?

Yes, you can! Just blend the cottage cheese until smooth before using it as a substitute.

Storage, Freezing & Reheating

Room temperature: Store the muffins in an airtight container on the counter for up to 3 days.
Refrigerator: Keep in a sealed container for up to 5 days. I like to warm them in the microwave for 10–15 seconds before eating to bring back that fresh-baked texture.
Freezer: These muffins freeze beautifully. Place them in a single layer on a baking sheet to freeze, then transfer to a freezer-safe bag or container for up to 3 months.
Reheating: Microwave frozen muffins for 20–30 seconds or let them thaw on the counter for a few hours. For a bakery-style feel, pop them in a 300°F oven for 8–10 minutes.

Healthy, gluten-free pumpkin muffins made with protein powder.

More Healthy Pumpkin Recipes You'll Love

Looking for other recipes like this? Try these:

Did you make this recipe?

If you make this recipe, be sure to comment and rate it down below. Also, don't forget to tag me @healthfulblondie on Instagram and use the hashtag #healthfulblondie so I can see your delicious creation and share it with my followers!

📖 Recipe

Comments

5 from 12 votes (5 ratings without comment)