November 17, 2018 2 Comments


These pumpkin spice protein cupcakes are beyond scrumptious! I can’t decide what I love most: the macros, the maple cream cheese frosting, or the moist spiced cake…. but at any rate, these are a must try if you’re a fan of pumpkin. I made these in the past but updated the recipe slightly to simplify the ingredients (replaced the applesauce for more pumpkin puree and added real maple syrup to the frosting). These tweaks didn’t change the nutrition much, but it did make frosting even richer and the cupcakes more pumpkin-y! I also updated the photos, because a recipe this good deserves beautiful photos 😉

Protein powder substitutions

I used Quest Protein Powder in Cinnamon Crunch for these cupcakes. You can use whatever whey you have on hand, but some work better than others. Whey blends (like Quest) that combine whey isolate, casein, and milk protein work best for baking! Whey concentrate comes in close second. Whey isolates are the absolute worst for baking. They always make baked goods come out spongey or dry (unless you use very little).

If you would rather not use protein powder, just double the amount of almond flour and coconut flour (use ½ cup each) and add more liquid (water or milk) if needed.

Flour substitutions

I opted for equal parts almond flour and coconut flour because it worked so well in that carrot cake last week (plus, it’s gluten-free)! However, you can substitute both flours for 2/3 cup of any of the following flours: all-purpose flour, brown rice flour, gluten-free baking blend, oat flour, spelt four, or whole wheat flour. If you only have almond flour, start with 3/4 cup and add more if the batter seems runny. If you only have coconut flour, use 6 tbsp. and add an additional tablespoon of oil or butter to avoid dryness. A note about coconut flour: the brand can make a huge difference in texture and flavor! I used Bob’s Red Mill Organic Coconut Flour.

I also added lots of fall spices like cinnamon, nutmeg, ginger and cloves, but you can just use 2 teaspoons of pumpkin spice if you don’t have all of these.

Sweetener substitutions

To sweeten these decadent cupcakes without adding much sugar, I used Pyure Organic Stevia Blend. This can be substituted for an equal measure of Truvia Spoonable, Truvia Baking Blend or twice as much baking stevia or coconut sugar. For the frosting, I used Swerve Confectioner’s Erythritol because it has the texture and flavor of powdered sugar; not to mention it’s calorie-free and all-natural! You can order Swerve online through Amazon, or sub baking stevia or half as much Pyure Organic Stevia Blend or Truvia Spoonable. You can also use liquid stevia drops to taste!

Maple cream cheese frosting

The frosting is cream cheese based, but the Greek whipped cream cheese can be swapped out for a dairy-free vegan brand like Daiya Foods or Go Veggie, making the entire recipe dairy-free and vegan! I added pure maple syrup to the frosting to make the frosting even richer, but you can use maple extract or vanilla extract if that’s all you have. If you’re not a fan of frosting, these make awesome muffins, too 😉

Just look at that tender crumb and thick creamy frosting! So good 🙂 I’ve posted the printable recipe for these Pumpkin Spice Protein Cupcakes below – I’d love your comments below if you try these!

This post contains affiliate links.

Pumpkin Spice Protein Cupcakes

These Pumpkin Spice Protein Cupcakes are full of rich pumpkin flavor and topped with maple cream cheese frosting. Gluten-free, low in fat, sugar, and carbs!
Course Dessert
Prep Time 15 minutes
Cook Time 20 minutes
Servings 12 cupcakes
Calories 131kcal


  • 3/4 cup (90g) cinnamon or vanilla whey blend* I used Quest brand in Cinnamon Crunch flavor
  • 1/4 cup almond flour*
  • 1/4 cup coconut flour*
  • 1/3 cup calorie-free sweetener* I used one that's twice as sweet as sugar
  • 2 tsp. baking powder
  • 1 tsp. ground cinnamon*
  • 1/2 tsp. ground nutmeg*
  • 1/2 tsp. ground ginger*
  • 1/4 tsp. ground cloves* or 2 tsp. pumpkin pie spice
  • 3/4 cup (6 large) egg whites
  • 1 1/2 cup 100% pure pumpkin
  • 1 tbsp. avocado oil or melted coconut oil, or buttery spread


  • 8 oz. whipped cream cheese or dairy-free cream cheese, softened at room temp
  • 1/2 cup powdered calorie-free sweetener I used Swerve Confectioner's Erythritol
  • 2 tbsp. pure maple syrup optional

*See blog post above for substitutions.


    • Preheat oven to 350 degrees F.
    • Whisk together dry ingredients (though spices) in a medium mixing bowl.
    • Add wet ingredients (through oil) and mix until just no clumps remain.
    • Lightly spray the wells of a muffin tin with cooking spray, or if using paper cupcake liners, lightly spray insides with cooking spray. You can also use silicone liners.
    • Divide batter between wells, filling 2/3 to the top.
    • Bake for 20-25 minutes until a toothpick or knife inserted comes out clean.
    • While cupcakes cool, combine frosting ingredients until smooth.
    • Spread frosting over cupcakes with a knife, or spoon batter into a sealable bag and cut off one corner to use as a “piping bag” for fancier cupcakes.
    • Store in the fridge in an airtight container up to one week.


    Calories (per cupcake, with frosting): 131kcal, Fat: 4.9g, Sat fat: 1.9g, Carbs: 10g, Fiber: 2g, Sugar: 5g, Protein: 12g, Sodium: 105mg

    2 Responses

    Sarah Wilkins
    Sarah Wilkins

    February 22, 2023

    Hi Lilliann! I am so glad to hear it’s a favorite :) You might also like these Funfetti Protein Cupcakes: https://nutritionistmom.com/blogs/blog/funfetti-protein-cupcakes


    February 22, 2023

    One of my favorite healthy treats! You don’t have to be so cautious or worried when you eat this. My taste buds were very satisfied.😋

    Leave a comment

    Comments will be approved before showing up.

    Also in Blog

    Collagen Cookie Skillet for Two

    February 13, 2024

    This Collagen Cookie Skillet for Two is the ultimate healthy Valentine's dessert! It's got chewy cookie edges, a gooey cookie center, and melty chocolate chips throughout. But that's not all - this giant cookie is also lower in sugar with added collagen protein, and gluten free and dairy free. Try it with protein ice cream for an extra protein boost!

    View full article →


    February 02, 2024

    This Chicken Shawarma & Mediterranean Vegetables has been on repeat for meal prep - it's so flavorful! Think spiced crispy chicken thighs with savory roasted vegetables, satisfying couscous, and dill yogurt sauce. This recipe can be made dairy-free using plain unsweetened coconut yogurt, or gluten-free using quinoa instead of the couscous. For vegan, you could try marinating tofu in the spices, olive oil, and lemon! However you make it, I hope you enjoy!

    View full article →

    Carrot Cake Baked Oatmeal (Vegan)

    January 30, 2024

    This Protein Carrot Cake Baked Oatmeal is such a treat to wake up to... it's even better cold! This baked oats recipe has warm spices, shredded carrots, plump raisins and yummy coconut (optional). It’s also vegan and gluten free, with a healthy serving of plant based protein. Yes, my obsession with carrot cake is real and this version did not disappoint!

    View full article →

    Get my FREE meal prep guide!

    Get family-friendly recipes, nutrition tips and faith-based inspiration delivered straight to your inbox.