If you’ve been searching for a cozy and nutritious treat, look no further than this High Protein Pumpkin Muffins with Greek Yogurt and Chocolate Chips Recipe. These muffins bring together the comforting flavors of fall pumpkin spices and the indulgent touch of chocolate chips, all while packing a protein punch thanks to Greek yogurt and protein powder. Perfect for breakfast, a snack, or a post-workout bite, they offer moist, tender crumb with a slight wholesome graininess from whole wheat flour and the subtle crunch of walnuts or pecans if you choose to add them. This recipe is one of my absolute favorites to bake when I want something filling yet delightfully tasty.

Ingredients You’ll Need
Every ingredient in this recipe is simple, approachable, and thoughtfully chosen to create the perfect balance of flavor, texture, and nutrition. Each component plays its part—pumpkin puree lends moisture and natural sweetness, Greek yogurt boosts protein and tenderness, and spices deliver warmth and heartiness.
- Pumpkin puree: Adds moisture and a beautiful earthy sweetness that defines the muffins.
- Plain Greek yogurt: Packs protein and keeps the muffins light and fluffy.
- Maple syrup or honey: Natural sweeteners that bring depth and subtle caramel notes.
- Eggs: Bind everything together and enrich the texture.
- Vanilla extract: Enhances all the flavors with a sweet fragrant hint.
- Whole wheat flour: Offers a hearty base with a touch of nuttiness and fiber.
- Protein powder (vanilla or unflavored): Boosts protein content to make these muffins truly satisfying.
- Baking soda and baking powder: Help the muffins rise beautifully and stay light.
- Ground cinnamon, nutmeg, and ginger: Warm spices that evoke classic pumpkin pie vibes.
- Salt: Balances sweetness and enhances the overall flavor.
- Chopped walnuts or pecans (optional): Add crunch and earthy flavor for extra texture.
- Mini dark chocolate chips (optional): Provide pockets of melty richness in every bite.
How to Make High Protein Pumpkin Muffins with Greek Yogurt and Chocolate Chips Recipe
Step 1: Prepare your oven and muffin tin
Start by preheating your oven to 350°F (175°C). This step ensures your oven reaches the perfect baking temperature so your muffins rise evenly and bake through without drying out. Line a muffin tin with 12 paper liners or give it a quick spray with cooking oil to prevent sticking.
Step 2: Mix the wet ingredients
In a large mixing bowl, blend together the pumpkin puree, Greek yogurt, maple syrup (or honey), eggs, and vanilla extract. Whisk until everything is smooth and homogenous. This mixture is the heart of your batter, delivering moisture and natural sweetness.
Step 3: Combine the dry ingredients
In a separate bowl, whisk together the whole wheat flour, protein powder, baking soda, baking powder, ground cinnamon, nutmeg, ginger, and salt. This dry blend ensures even distribution of leavening agents and spices, giving your muffins the signature warm aroma and perfect texture.
Step 4: Merge wet and dry ingredients
Gradually add the dry ingredients to the wet mixture. Stir gently until just combined—avoid over-mixing to keep your muffins tender and light instead of dense.
Step 5: Add the extras
Fold in the chopped walnuts or pecans and mini dark chocolate chips if you’re using them. These optional add-ins bring wonderful texture and surprise bursts of flavor that brighten every bite.
Step 6: Fill the muffin cups
Divide the batter evenly among the prepared muffin cups, filling each about two-thirds full. This leaves enough room for the muffins to rise without spilling over.
Step 7: Bake your muffins
Place the tin in your preheated oven and bake for 18 to 22 minutes. You’ll know they’re done when a toothpick inserted into the center comes out clean, signaling those perfect fluffy centers.
Step 8: Cool before enjoying
After removing from the oven, let the muffins cool in the tin for about 5 minutes. Then transfer them to a wire rack to cool completely. Cooling prevents them from becoming soggy and enhances the texture.
How to Serve High Protein Pumpkin Muffins with Greek Yogurt and Chocolate Chips Recipe

Garnishes
Top your muffins with a light dusting of cinnamon powder or a smear of Greek yogurt mixed with a drizzle of honey for extra tangy creaminess. A simple sprinkle of chopped nuts can also elevate the presentation and add crunch.
Side Dishes
These muffins pair brilliantly with fresh fruit such as apple slices or a handful of berries. A warm cup of coffee, chai tea, or even a protein smoothie transforms your muffin snack into a balanced, energized mini-meal.
Creative Ways to Present
For parties or brunches, consider stacking muffins on a tiered tray or serving them wrapped individually in parchment paper tied with twine for a rustic look. You can also split muffins and fill them with a smear of nut butter for an extra dose of protein and flavor.
Make Ahead and Storage
Storing Leftovers
Store any leftover muffins in an airtight container at room temperature for up to 3 days. They stay moist and fresh, making them an easy grab-and-go option for busy mornings.
Freezing
If you want to keep these muffins longer, freeze them individually wrapped in plastic wrap and then placed in a freezer bag. They can be frozen for up to 3 months without losing much flavor or texture.
Reheating
When ready to eat, thaw muffins at room temperature or pop them in the microwave for about 20 seconds to enjoy warm, soft bites just like fresh from the oven.
FAQs
Can I use canned pumpkin?
Absolutely! Canned pumpkin puree works perfectly for this recipe. Just make sure it’s pure pumpkin and not pumpkin pie filling, which contains added spices and sweeteners.
What type of protein powder works best?
Vanilla or unflavored protein powders blend seamlessly here. Choose your favorite brand, whether whey, plant-based, or collagen, depending on your dietary preferences.
Can I substitute the sweetener?
Yes, you can swap maple syrup or honey with agave nectar or even coconut sugar. Just keep in mind that changing sweeteners may slightly affect the moisture and taste.
Are the nuts and chocolate chips necessary?
Not at all! They are optional but recommended for texture and flavor contrast. If you’re nut-free, simply omit the nuts or replace them with seeds like pumpkin or sunflower seeds.
How do I make these muffins vegan?
To make a vegan version, use a flax or chia egg substitute and replace Greek yogurt with dairy-free yogurt. Use maple syrup instead of honey to keep everything plant-based.
Final Thoughts
There you have it—your go-to High Protein Pumpkin Muffins with Greek Yogurt and Chocolate Chips Recipe that’s as satisfying as it is nourishing. Whether you’re fueling a busy day or craving a sweet snack that won’t weigh you down, these muffins deliver on both taste and nutrition. I hope you enjoy baking and sharing these as much as I do. Trust me, they’ll quickly become a beloved staple in your kitchen!
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High Protein Pumpkin Muffins with Greek Yogurt and Chocolate Chips Recipe
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Total Time: 35 minutes
- Yield: 12 muffins
- Category: Breakfast
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
These high protein pumpkin muffins are a delicious and nutritious treat, blending pumpkin puree and Greek yogurt with whole wheat flour and protein powder for a wholesome snack or breakfast option. With aromatic spices and optional nuts and chocolate chips, they offer a perfect balance of flavor and health benefits.
Ingredients
Wet Ingredients
- 1 cup pumpkin puree
- 1/2 cup plain Greek yogurt
- 1/3 cup maple syrup or honey
- 2 large eggs
- 1 teaspoon vanilla extract
Dry Ingredients
- 1 1/2 cups whole wheat flour
- 1 scoop protein powder (vanilla or unflavored)
- 1 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1 teaspoon ground cinnamon
- 1/2 teaspoon ground nutmeg
- 1/4 teaspoon ground ginger
- 1/4 teaspoon salt
Optional Ingredients
- 1/2 cup chopped walnuts or pecans
- 1/2 cup mini dark chocolate chips
Instructions
- Preheat the oven: Preheat your oven to 350°F (175°C). Line a muffin tin with 12 paper liners or lightly grease it with cooking spray to prevent sticking.
- Combine wet ingredients: In a large mixing bowl, whisk together the pumpkin puree, Greek yogurt, maple syrup (or honey), eggs, and vanilla extract until the mixture is smooth and well combined.
- Mix dry ingredients: In a separate bowl, whisk together the whole wheat flour, protein powder, baking soda, baking powder, ground cinnamon, ground nutmeg, ground ginger, and salt to combine the dry ingredients evenly.
- Combine wet and dry mixes: Gradually add the dry ingredients into the wet ingredients, stirring gently and just until combined. Avoid over-mixing to keep the muffins tender.
- Fold in extras: If using, gently fold in the chopped walnuts or pecans and mini dark chocolate chips to distribute them evenly throughout the batter.
- Fill muffin cups: Divide the batter evenly among the 12 prepared muffin cups, filling each about two-thirds full to allow room for rising.
- Bake: Bake the muffins in the preheated oven for 18 to 22 minutes or until a toothpick inserted into the center comes out clean, indicating they are fully baked.
- Cool muffins: Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely before serving or storing.
Notes
- Use unsweetened pumpkin puree for best flavor and nutrition.
- You can substitute protein powder with your favorite type, but unflavored or vanilla works best to maintain taste balance.
- Optional nuts and chocolate chips add texture and flavor but can be omitted for a simpler muffin.
- Store muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to 1 week.
- These muffins freeze well; wrap individually and freeze for up to 3 months.
- For a vegan version, substitute eggs with flax eggs and use a plant-based yogurt and protein powder.

