By Easy and quick to make, these high-protein pumpkin muffins are a healthier version of the infamous Starbucks muffins. They're filled with a cream cheese center and topped with crunchy and nutty pepitas. Extra bonus: they have more fiber and half the sugar of their store-bought counterparts!
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I've always been a sucker for a good muffin, but finding one that actually keeps me full and satisfied without a sugar crash used to feel like a quest for the Holy Grail. And pumpkin? Well, that's a non-negotiable when the leaves start to turn. I tinkered with this recipe for ages, determined to get a muffin that's as good as bakery muffins.
After many (many!) test batches, tweaking the spices, perfecting the batter consistency, and figuring out the ideal filling-to-muffin ratio, these beauties were born! They're a far cry from your average dry, underwhelming protein muffin.
These are substantial, flavorful, and a recipe I'm truly proud to share from our collection of high protein breakfast recipes. Let's cook!
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how to nail the cream cheese filling
For truly amazing high-protein pumpkin muffins, make sure your cream cheese is fully softened for a lump-free, silky filling. Then, pipe it in confidently into the center of each muffin - and don't be afraid to overfill! Side note - this filling is also delish in our high protein blueberry muffins!
ingredient notes & substitutions
All substitutions are a 1:1 substitute unless otherwise noted. See the recipe card for quantities.
- Almond Flour: Adds a bit of extra protein and healthy fats.
- All-Purpose Flour: Provides the main structure for our muffins. A 1:1 gluten-free flour will work too.
- Cinnamon and pumpkin pie spice: Must-haves for fall baked goods!
- Baking Powder and soda: Our primary leavening agents, helping the muffins rise tall and become fluffy.
- Salt and vanilla extract: Balances the sweetness and enhances all the other flavors. Never skip the salt or vanilla in baking!
- Maple Syrup: Our natural sweetener of choice here. You can substitute this but it has to be a liquid sweetener.
- Canned Pumpkin: The star of the show! Make sure you grab pure pumpkin puree, not pumpkin pie filling, which has added sugars and spices. Use leftovers to make breakfast cookies, protein pumpkin pie, or a pumpkin spice latte shake!
- Greek Yogurt: This adds a significant protein boost, moisture, and a lovely tang that balances the sweetness. It also helps activate the baking soda.
- Large Eggs: Bind the ingredients together, provide structure, add richness, and contribute to the protein content.
- Cream Cheese: Make sure it's softened so it mixes smoothly.
This recipe has not been tested with other substitutions or variations. If you replace or add any ingredients, please let us know how it turned out in the comments below!
high protein ingredient spotlight: Greek yogurt
Let's talk about Greek yogurt! This isn't just here for show; it's one of our favorite ingredients for our high-protein recipes. A typical serving (around 7 ounces) can pack a hefty 20 grams of protein. It's an ingredient we use in all sorts of stuff, from Greek yogurt pancakes to key lime pie!
here's how to make pumpkin protein muffins
Be sure to scroll to the recipe card for the full muffin recipe!
- Whisk together the dry batter ingredients in a big bowl.
- Combine the wet ingredients in a separate bowl. Mix 'em up until they're just combined.
- Combine the wet and dry ingredients.
- Fill up the muffin cups ⅔rds with batter.
- Make the cream cheese filling by beating together the filling ingredients until smooth.
- Pipe in the cream cheese filling into the center of the pumpkin batter using a piping bag or ziplock bag with the end cut off. Top with peptias.
- Bake for 20 minutes. Then let them cool before enjoying!
quick recipe video
using a silicone muffin tin (and tips for not)
I love not using paper cups because muffins are so much easier to remove from silicone tins! If not using silicon, be sure to spray paper liners with non-stick spray or use foil liners.
troubleshooting & testing notes
Filling consistency
Our first few tests had the filling either too runny (it disappeared into the muffin) or too thick (it didn't meld well). Adding that little bit of flour to the cream cheese mixture was the ticket to getting it just right - stable enough to hold its shape but still creamy.
how to store & meal prep it
These muffins are great to make a batch to enjoy as a quick breakfast or snack for the week!
- Fridge: Store leftover muffins in an airtight container in the refrigerator for up to 6 days. The cream cheese filling means they definitely need to be kept chilled.
- Freezer: Yes, you can freeze them! Once completely cooled, wrap individual muffins tightly in plastic wrap and then place them in a freezer-safe bag or container. They'll keep well for up to 2-3 months.
- Reheating: You can enjoy them chilled straight from the fridge, or if you prefer a warm muffin, microwave for about 15-20 seconds, or until warmed through. You can also warm them in a 300°F (150°C) oven for about 5-7 minutes. You can also reheat from frozen.
enjoy these with...
I love muffins for breakfast, but I usually pair them with a lil' something else. Some great pairings include our Cottage Cheese Egg Bites, Chipotle Breakfast Burritos, and Protein Coffee without Protein Powder!
Recipe
high-protein pumpkin muffins with cream cheese filling
Ingredients
- ½ cup almond flour
- 1.5 cups all-purpose flour
- 1 teaspoon cinnamon
- 1 tablespoon pumpkin pie spice (*)
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 teaspoon salt
- 1 teaspoon vanilla extract
- ¾ cup maple syrup
- 15 oz pumpkin puree (1 can)
- ½ cup greek yogurt
- 2 eggs (large)
- pepitas for topping (I used about ⅓ of a cup)
Filling
- 8 oz cream cheese (softened)
- 3 tablespoon maple syrup
- 2 tablespoon all-purpose flour
- 1 egg
- 1.5 teaspoon vanilla extract
- ¼ teaspoon salt
Before you start!
If you make this recipe, please take a moment to leave us a review. We love to hear from you!
Instructions
- Preheat the oven to 350 degrees. Line a muffin tin with any muffin liner you prefer. It's nice to have bakery-style (high sides) liners, but it's not necessary. If using paper liners, spray them well with non-stick spray, or use silicone muffin tins or foil liners.
- Combine ½ cup almond flour, 1.5 cups all-purpose flour, 1 teaspoon cinnamon, 1 tablespoon pumpkin pie spice, 1 teaspoon baking powder, 1 teaspoon baking soda, and 1 teaspoon salt in a large bowl.
- In a separate bowl, mix together the 1 teaspoon vanilla extract, ¾ cup maple syrup, 15 oz pumpkin puree, ½ cup greek yogurt, and 2 eggs. Pour this into the dry ingredients and mix until a thick batter forms. No need to overmix - just until everything is incorporated.
- Fill the muffin tins almost to the top with batter. These are meant to be bakery style muffins with a nice rise and you should have enough batter for 12 muffins.
- Next, make the filling. Use a hand mixer to beat together the 8 oz cream cheese, 3 tablespoon maple syrup, 2 tablespoon all-purpose flour, 1 egg, 1.5 teaspoon vanilla extract, and ¼ teaspoon salt in a bowl.
- Transfer this to a piping bag or to a ziplock bag and cut the tip off. Squeeze about 2 tablespoons of filling into the center of each muffin by pushing the tip down into the batter. The batter will rise up around the filling - that's perfect! Just keep piping until you've used all the cream cheese filling! Top with pumpkin seeds around the edge before baking.
- Bake the muffins for 20 minutes at 350 degrees or until golden brown. Remove from the oven and let cool for 5 minutes before letting them cool completely on a wire rack.
Video
Notes
Looking for more information?
Additional substitution information can be found above in the substitution section of this post.
Nutrition Disclaimer
Nutritional information is an estimate and for informational purposes only.
Such a delicious treat. Thank you for sharing your recipe with me ❤️🥰
So happy to hear that!
Tried this recipe and it was delicious! I did have a little trouble with the muffins not cooking all the way but I think it was because I tried to bake all 12 muffins at once in one pan. Next time I think I'll try to make this recipe but as pumpkin bread. Hopefully it comes out just as good!
I think baking them in every other space will definitely fix that! Also, those bakery style liners can help too if you bake them all together.
Very good. I think I will add a little more spice to the cake, and possibly the cream cheese filling. I really liked that it was higher in protein. Thank you!
So glad you enjoyed!
Made these muffins yesterday, so tasty! Had all the ingredients on hand except the almond flour, but Aldi has a good price on a bag of almond flour. Definitely will be making these again.
Thats great to hear!
I made these muffins today. They are so delicious! The recipe is a few more steps than I normally like but know that it's very much worth it! They are not sweet and are so good just out of the oven (after cooling a few minutes). I would note one thing: The recipe does not mention pepitas, but you can see them in the pics. I had some on hand, so I used them They got very crispy from baking. So yummy!
Can I use stevia instead of maple syrup? If so how much?
You can but it's not a 1:1 swap and I haven't tested it. In general, 1/4c of maple syrup = 1/8-1/4 tsp of stevia but you'll need to add 2-3 more tbsps of greek yogurt to the batter to make up that missing moisture. If possible, I would try to find a stevia maple syrup, sugar free syrup, or monk fruit maple syrup (my favorite).
What can I use instead of almond flour?
Oat flour works just fine or whole wheat!
very pleased with this recipe! been GF for 20+ years and wanting more nutrient dense recipes - especially baked goods that don't leave me feeling hungry after. The flavor and texture were great - TBH I have never had a Starbucks one of these, so I don't have that comparison. But it was a real treat to make and have these muffins! I will be trying more recipes from this site.
Thats awesome to hear! Thanks so much!
Oh my god. Words cannot describe the nostalgia I felt eating this muffin. Hands down one of my new favorite recipes of all time. Thank you so so much for bringing me back to my favorite childhood Starbucks treat, but with wholesome and feel-good ingredients! I feel forever in debt to you🙏
That just makes my heart sing!!
I can't get over how delicious these are! Mine didn't dome nicely (maybe because of old baking powder?) and spread quite a bit instead. Next time I'm going to try doing every other well in the muffin tin to see if it helps them come out prettier. I froze most of the batch, but have taken one or two out every evening all week since I'm happily reaching for them every day. These are definitely going to be in regular breakfast rotation!
Amazing! Yes, the muffin every other is key to not having them spread! Everytime I'm rushed and doing do it every other muffin tin, they spread on me. Thankfully still just as delicious!
Just made these, but didn't have cream cheese. I made a substitute with cream cheese, greek yogurt, and butter, but kept the rest of the filling recipe the same. It was very liquidy and most of it ended up baking into the muffin because of that instead of staying as its own layer, but it was still very yummy. I'll have to try again with actual cream cheese next time!
These are great and easy! And the kitchen smells so good with cinnamon and nutmeg!
These turned out perfect!!!
Amazing!!
So delicious! My whole family loves these
That's great to hear!!