Chocolate Pumpkin Protein Cupcakes with a protein pumpkin filling and protein chocolate frosting! Full of pumpkin spice flavor, these cupcakes are healthy, low fat and sugar-free too.

Took my two tries to nail this recipe, but these cupcakes – with the chocolate and pumpkin together – were definitely worth it! Super soft cupcakes with the pumpkin flavor in the cupcake and filling too. Very much worth it.

Ingredients for Chocolate Pumpkin Protein Cupcakes

These chocolate pumpkin protein cupcakes are made with healthy ingredients, sweetened with protein powder, filled with protein pumpkin mix and topped with a protein chocolate frosting. Here’s what you need for these healthy cupcakes:

For the Chocolate Pumpkin Spice Protein Cupcake

Pure Pumpkin Puree either from the can like Libby’s, or homemade. Make sure its not pumpkin pie filling though

Chocolate Protein Powder needed for a high protein cupcake and also replaces the ‘sugar’.
I used Whey-Casein Chocolate protein powder from Quest Nutrition and Whey protein powder from Prozis for this recipe.
Dymatize ISO is another good option for the Whey.
Whole Wheat Pastry Flour
Unsweetened Cocoa Powder
1:1 Zero Calorie Sugar Substitute – I use Lakanto, to keep this recipe sugar free; (code HAYLSKITCHEN for a discount here)
Hot Water
Some Lemon Juice
A bit of Melted Butter
Baking Soda

The Protein Pumpkin Mix to fill in:

Pure Pumpkin Puree
Vanilla Protein Powder: I used Quest Nutrition Vanilla whey-casein here.
Some Almond Milk

For the Protein Chocolate Frosting:

Chocolate Protein Powder: I recommend Quest Nutrition Chocolate here since it’s whey-casein and blends well with the yogurt.
Unsweetened Cocoa Powder
Non-fat Greek Yogurt

Tips for the perfect Chocolate Pumpkin Cupcakes Recipe with Protein Powder

While this protein powder chocolate pumpkin cupcake recipe is easy, there are a few things to keep in mind:

Grease the cupcake liners if they aren’t silicon.
This will allow the protein powder cupcakes to come off easily.

Use pumpkin puree, not pumpkin pie mix; The pie mix is already sweetened, and not what you want here.

Use melted Butter so that it mixes well into the healthy chocolate pumpkin spice cupcake batter.

Don’t over-mix the batter!
Make sure you gently fold the dry mix into the wet to combine them.
If you over-mix it, the protein powder will make the low calorie protein pumpkin cupcakes tough, dense and gummy.

Taste the batter and see if you need some extra sweetener. I’d recommend using stevia powder to maintain the consistency of the batter and have sugar free and healthy cupcakes.

Don’t let the batter sit out too long; Pour immediately into baking pan and bake.
This is to avoid any reactions between the ingredients.

Don’t over-fill baking pan cavities or the cupcake batter will overflow!

Don’t over-bake the mini cake bites or they might get tough; Remove when the tester/knife comes out just dry; Little moisture is okay.

Let stuffed cupcakes cool completely before filling and frosting, or the filling and frosting will melt away.

Add milk in the filling little at a time – too much will give you a very runny mixture.

How to Store Chocolate Pumpkin Spice Cupcakes

This chocolate pumpkin spice cupcake recipe is a good meal prep snack or dessert and can be stored on the counter, in the fridge or freezer too.

Place chocolate pumpkin cupcakes with filling in an airtight container and you can keep them on the countertop for 2-3 hours, fridge for 5 days or freezer for 2-3 months.

To defrost frozen chocolate pumpkin spice protein cupcakes, leave them on the countertop or place them in the fridge overnight. I would not recommend using the microwave.

Alternatives for Healthy Chocolate Pumpkin Cupcakes

I made these healthy chocolate pumpkin cupcakes low fat, low calorie and sugar free with the set of ingredients above, but here’s some options to try. I havn’t given them all a go yet, so I can’t say how they all would work.

Whole Wheat Pastry Flour: Use All purpose flour or 1:1 Gluten Free Baking Flour in the same amount by weight not cups.
1:1 Zero Calorie Sugar Replacement: Regular confectioners sugar or coconut sugar (this won’t be sugar free though, and also higher in calories)
Melted Butter: Melted Coconut Oil or Dairy Free Butter
Lemon Juice: Apple Cider Vinegar or White Vinegar

Alternatives for Cupcake Fililng:

Almond Milk: Regular milk

Options for Cupcake Frosting:

Greek Yogurt: Coconut Yogurt

For a Vegan Chocolate Pumpkin Cupcake Recipe:

Use a plant based protein powder, dairy free butter and coconut yogurt as alternatives and turn this chocolate pumpkin cupcake recipe Vegan!

Some Unique Cupcake Recipes with Protein Powder

More Pumpkin Protein Powder desserts: