Pumpkin Chocolate Chip Muffins
If you love pumpkin and chocolate, these pumpkin chocolate chip muffins take the classic fall favorite and give it a high-protein upgrade, making them just as satisfying as they are nourishing. Thanks to blended cottage cheese, these muffins stay incredibly moist and tender without needing heavy cream or excessive oil. You don’t taste it at all!
The muffins are naturally sweetened with coconut sugar, loaded with melty chocolate chips, and finished with a crunchy streusel topping that makes every bite irresistible. For anyone who craves chocolate chip pumpkin muffins, these are guaranteed to be on repeat all season long.
If you make a batch of these chocolate chip pumpkin muffins, don’t miss out on my pumpkin crumb cake donuts and pumpkin cheesecake protein donuts, too!
Why You’ll Love This Recipe
- Texture: Thanks to the blended cottage cheese, these muffins turn out moist and fluffy without the need for lots of butter.
- Streusel topping: I swap the classic sugar topping for a sweet, crumbly streusel that gives the muffins even more texture and flavor, enhancing the bakery-style feel.
- Naturally sweetened: Sweetened with coconut sugar and monk fruit sweetener, these pumpkin chocolate chip muffins are refined sugar-free.
- Quick and easy: Made in a large bowl and ready in 30 minutes, these muffins are fuss-free and foolproof.
- Freezer-friendly: Leftovers store and freeze well, so you can always have a stash on hand for fall mornings.
Ingredients You’ll Need for these bakery-style muffins
These pumpkin chocolate chip muffins come together with simple ingredients. Here are a few of my notes:
- Pumpkin Puree: Make sure you’re grabbing 100% pure pumpkin puree, not pumpkin pie filling. They sit right next to each other on the shelf, but pie filling is pre-sweetened and spiced, and it’ll throw off the whole recipe. Fresh pumpkin puree can also be used. Just be sure to drain excess moisture.
- Cottage Cheese: This is where the protein and moisture come from. Blending it with a little melted coconut oil before it goes into the batter smooths out the curds completely, so you get a tender crumb with zero curdy texture.
- Coconut Sugar: Sweetens the muffins with a deeper, almost caramel-like flavor than white sugar. Regular brown sugar or maple sugar both work as a swap. Maple sugar or regular brown sugar work well too, offering a slightly different sweetness.
- Coconut Oil: Adds richness and keeps the muffins moist. Melted butter, olive oil or avocado oil are easy subs.
- Flour: I use all-purpose flour for the base of the muffin batter. Use a gluten-free 1:1 flour blend to make these muffins gluten-free.
- Pumpkin Spice: If you’re out, a mix of cinnamon, nutmeg, ginger, and a pinch of cloves gets you there.
- Chocolate Chips: I typically use regular chocolate chips here, but mini chips are also great. Dark chocolate chips are my go-to, but semisweet chocolate chips, milk chocolate chips, or even white chocolate chips work. Feel free to swap the chocolate chips with chopped pecans or chopped walnuts for a nutty taste and crunchy texture.
- Streusel Topping: This is what takes these from “good muffin” to “bakery muffin.” Don’t skip it! The coconut sugar and monkfruit blend gives it a light crunch instead of a heavy crumb.
How to Make Pumpkin Chocolate Chip Muffins
These pumpkin muffins with chocolate chips are the easiest muffins you’ll ever make! All you need are a few mixing bowls and a muffin pan.
Step 1: Combine ingredients. Whisk the coconut sugar and oil in a large bowl. Then, add the remaining wet ingredients, and mix to combine. Whisk the dry ingredients in a second bowl. Then, fold the dry ingredients into the wet ingredients just until no streaks remain. Be careful not to overmix! Fold in the chocolate chips.
Step 2: Portion. Divide the muffin batter evenly between a greased muffin tin, filling each cavity 2/3 of the way full. I like to use a cookie scoop for even portions!
Step 3: Layer. Sprinkle the streusel mixture evenly over each muffin.
Step 4: Bake. Transfer the muffins to the oven, and bake until they’re golden brown and tall. A toothpick inserted into the center should come out clean.
Step 5: Cool. Let the muffins cool in the pan slightly. Then, transfer them to a wire rack to cool completely. This helps them hold their shape!
Make Mini Pumpkin Chocolate Chip Muffins
Combine the batter as usual. Then, fill mini muffin cups about 2/3 of the way full, and bake, beginning to check for doneness around 10-12 minutes.
Recipe Tips
- Blend the cottage cheese for a smooth texture. Cottage cheese is packed with protein, but can have a slightly curdy texture. Blending it with a little melted coconut oil before adding it to the muffin batter ensures a completely smooth and creamy consistency when making pumpkin chocolate chip muffins.
- Don’t overmix the batter. Overmixing can make muffins tough instead of light and fluffy. Gently stir the dry ingredients into the wet until just combined. A few lumps are okay! This keeps the muffins soft and tender, which is especially important with pumpkin chocolate chip muffins.
- Don’t overfill the muffin cups. The batter will rise in the oven. So, filling each cavity just ? of the way full helps prevent the batter from spilling over and burning.
- Use room temperature ingredients. Let your eggs and pumpkin puree sit out for about 10 minutes before mixing. This helps everything blend more smoothly and creates a better texture in your muffins.
- Check for doneness with a toothpick. Since cottage cheese adds extra moisture, these muffins may take a little longer to bake. Insert a toothpick into the center of the muffin to check for doneness. If it comes out clean or with just a few crumbs, they’re ready. If the batter sticks, bake for another 1-2 minutes and check again.
How to Store
I love to keep these muffins on hand for quick grab-and-go snacks!
Freezer: Freeze pumpkin chocolate chip muffins in a single layer, then transfer to a freezer bag for up to 3 months. Let them thaw at room temperature or microwave for 30 seconds before enjoying.
Room Temperature: Store the pumpkin chocolate chip muffins in an airtight container for up to 2 days.
Refrigerator: Keep the muffins in an airtight container for up to 8 days. Warm slightly before serving for the best texture.
More Muffin Recipes

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Cottage Cheese Pumpkin Chocolate Chip Muffins
Ingredients
Muffin Base:
- 1 cup pumpkin puree
- 1/2 cup coconut sugar
- 1/2 cup coconut oil melted
- 2 large eggs
- 1 tsp vanilla bean paste
- 1 cup cottage cheese blended with 2 tbsp melted coconut oil
- 1 1/2 cups all-purpose flour
- 1 tsp baking soda
- 1/2 tsp baking powder
- 1 tsp pumpkin spice
- 1/2 cup chocolate chips
Streusel Topping:
- 1/3 cup coconut sugar
- 3 tbsp coconut oil
- 1/3 cup monkfruit sweetener granulated
- 4 tbsp gluten free 1:1 flour
Instructions
Enable step-by-step mode- Preheat your oven to 350°F (175°C). Line a muffin tin with liners or lightly grease it.
- In a large bowl, combine the coconut sugar and oil and whisk to combine
- Add in the pumpkin puree, eggs, vanilla extract, and cottage cheese and mix until well combined
- In another bowl, whisk together the flour, baking soda, baking powder, pumpkin pie spice, and a pinch of salt
- Gently add the dry ingredients to the wet mixture, stirring until just combined (be careful not to overmix)
- Fold in the chocolate chips
- Scoop the batter into the prepared muffin tin with a 3 inch cookie scoop, filling each cup about 2/3 full
- Sprinkle the streusel topping on each muffin
- Bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean
- Allow to cool in the muffin tin for a few minutes before transferring to a wire rack to cool completely
