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Home » Recipes » Muffins

Chocolate Pumpkin Protein Muffins – Amazing and Healthy!

Published: Sep 16, 2022 · Last Modified: Feb 21, 2025 by Haylee Jane Monteiro · This post may contain affiliate links

Amazing Chocolate Pumpkin Protein Muffins with the fall flavor and chocolate, for an indulgent cozy treat! Healthy chocolate pumpkin muffins use protein powder for sweetness and have no sugar, oil or butter.

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Amazing Chocolate Pumpkin Protein Muffins with the fall flavor and chocolate, for an indulgent cozy treat! Healthy chocolate pumpkin muffins use protein powder for sweetness and have no sugar, oil or butter.

Chocolate and pumpkin really is an underrated combination – the hint of pumpkin spice in the rich chocolate flavor – so good!

A very clean and cozy fall recipe here though.

Ingredients for Chocolate Pumpkin Protein Muffins:

This recipe for chocolate pumpkin protein muffins is as healthy as it gets with no oil or butter and no sugar either.

Here’s what you need to make a batch of this good stuff:

  • Pumpkin Puree
  • Chocolate Protein Powder as a replacement for the sugar – this is what makes this a sugarfree chocolate protein muffin recipe; I use Quest Nutrition Chocolate here.
  • Unflavored Protein Powder to replace some of the flour (and carbs) in the recipe for a slightly lower carb high protein brownie. I used Quest Nutriton Multi-purpose here.
  • Unsweetened Cocoa Powder
  • Whole Wheat Pastry Flour for a healthy, nutritious and whole grain muffin recipe.
  • Non-fat Greek Yogurt to add even more protein and keep these low fat
  • Almond Milk for some moisture
    Also makes this a dairy free muffin recipe. Feel fee to use any other non dairy or normal milk
  • Eggs
  • Stevia Sweetener
  • Vanilla Extract
  • Baking Soda and Baking Powder – you need them both for that perfect rise!
  • Pumpkin Pie Spice

And then for the mix-ins

  • Sugar free Chocolate Chips or Chopped Chocolate – I use sugar free ones from Lakanto here (HAYLSKITCHEN for a discount here as well). Lily’s is another sugar-free option!
Amazing Chocolate Pumpkin Protein Muffins with the fall flavor and chocolate, for an indulgent cozy treat! Healthy chocolate pumpkin muffins use protein powder for sweetness and have no sugar, oil or butter.

Things to keep in mind for these Chocolate Pumpkin Muffins with Protein Powder

This recipe for chocolate pumpkin protein powder muffins really is quite easy, but here’s some tips to get them perfectly light and fluffy.

  • Use pumpkin puree, not pumpkin pie mix so there’s no added sugars in the recipe
  • Don’t overmix the batter!
    Pour the dry mix into the dry and just fold them together or too much gluten will develop, again giving you dense and gummy muffins. The protein powder could also cause toughness.
  • Don’t skip out on the almond milk or the yogurt
    They add a fair bit of moisture to the muffins since there’s no oil here, also the protein powder in the muffins needs extra moisture.
  • Spray the insides of the muffin pan with oil spray so the muffins come off easily.
  • For the perfect rise, bake the muffins at 425F for 5 mins, and then another 15-18 minutes at 350F.
    That initial hot air makes the tops rise, and then the lower temperature lets the muffins continue to cook on the inside.

Can you store Weight Watchers Chocolate Pumpkin Muffins?

With such a low calorie and reduced fat recipe, these weight watcher-friendly chocolate pumpkin muffins with are completely to okay to indulge in; I myself had nearly 2 at a time!

You can keep the weight watchers chocolate pumpkin muffins out at room temperature on the countertop for 2 or 3 days, or in the fridge for or 4 or 5 days. Be sure to use an airtight container.

To freeze the healthy chocolate pumpkin muffins, wrap them plastic wrap, and place in a freezer-safe zipper bag. They’ll last for 2 or 3 months. Thaw them when you want fall spiced apple dessert at Thanksgiving!

Amazing Chocolate Pumpkin Protein Muffins with the fall flavor and chocolate, for an indulgent cozy treat! Healthy chocolate pumpkin muffins use protein powder for sweetness and have no sugar, oil or butter.

Some alternatives for these Healthy Chocolate Pumpkin Muffins:

I made these healthy chocolate pumpkin mufffins with the whole wheat pastry flour and protein powder as described, but here’s some other clean ingredients to try:

  • Whole Wheat Pastry Flour: All purpose flour or 1:1 Gluten Free Baking Flour, in the same amount by weight not cups.
  • Unflavored Protein Powder: 45g more Flour, but also reduce yogurt to ½ cup (112g)
  • Greek Yogurt: Coconut Yogurt
  • Almond Milk: Any other milk 
  • Stevia Sweetener: Monkfruit sweetener (I use the one from Lakanto; Code HAYLSKITCHEN gives you a discount here) or regular sugar

Some more Protein Muffin Recipes to try:

  • Spinach Protein Muffins
  • Oil Free Apple Protein Muffins
  • Chocolate Stuffed Churro Protein Muffins
  • Low Calorie Chocolate Protein Muffins
  • Cranberry Eggnog Protein Muffins
  • Blueberry Sausage Protein Muffins
  • Protein Monkey Bread Muffins

And some more high protein Pumpkin recipes:

  • Single Serve Protein Pumpkin Pie
  • No Bake Pumpkin Protein Bars
  • Pumpkin Cream Cheese Protein Muffins (The Best Starbucks Copycat)
  • Pumpkin Protein Cinnamon Rolls
  • Chocolate Lava Pumpkin Protein Cookie
  • Protein Pumpkin Cake with Cream Cheese Frosting

Chocolate Pumpkin Protein Muffins

5 from 1 vote
Print recipe Pin Recipe
Prep Time10 minutes mins
Cook Time18 minutes mins
Total Time28 minutes mins
Servings: 14 muffins
Calories: 102kcal
Course: Breakfast, Dessert, Post-Workout
Cuisine: American
Amazing Chocolate Pumpkin Protein Muffins with the fall flavor and chocolate, for an indulgent cozy treat! Healthy chocolate pumpkin muffins use protein powder for sweetness and have no sugar, oil or butter.

Ingredients

  • 1 cups Whole Wheat Pastry Flour, 120g
  • ⅔ cup Chocolate Protein Powder, Whey-casein, 60g, 2 scoops
  • ½ cup Unflavored Protein Powder, Whey-casein, 45g
  • ½ cup Unsweetened Cocoa Powder, 40g
  • Stevia Sweetener, 3 tablespoon sugar worth (Use your brand’s Conversion Chart)
  • 2 teaspoon Baking Powder
  • 1 teaspoon Baking Soda
  • 1 tablespoon Pumpkin Pie Spice
  • 1 cup Pumpkin Puree, 240g, Not pumpkin pie mix
  • ¾ cup Non-fat Green Yogurt, 168g
  • ½ cup Unsweetened Almond Milk, 120ml
  • 3 Eggs
  • 1 teaspoon Vanilla Extract
  • 2 tablespoon Chopped Chocolate or Chocolate Chips, Sugar-free recommended below, about 28g
  • Optional Pumpkin Seeds, for topping

Instructions

  • Preheat oven to 425°F, grease 14 muffin cups – 12-cup pan and 2 more with cooking spray.
  • In a large bowl, whisk together whole wheat pastry flour, chocolate protein powder, unflavored protein powder, cocoa powder, stevia sweetener, baking powder, baking soda and pumpkin pie spice.
  • In another bowl, whisk pumpkin puree, Greek yogurt, almond milk, eggs and vanilla.
  • Add dry mix to wet, and gently fold until combined.
  • Add most chocolate chips (reserve some for top) into batter, and gently fold again.
    DO NOT OVER-MIX or too much gluten will form from the wheat flour, and make the muffins dense.
  • Divide the batter among muffin cups, about ¾ way to the top.
    Top with remaining chocolate and pumpkin seeds.
  • Bake for 5 minutes, then reduce temperature to 350°F (leaving muffins in oven) and bake another 13-15 minutes (total of 18-23 min).
    A toothpick inserted into center should come out dry.
  • Cool for 10 minutes, then remove pan. Transfer to a wire rack to cool completely, about 15 minutes, and enjoy.

Notes

  • Nutrition value is calculated using products recommended below.
  • See post for alternate ingredients, tips and storage options.
Product Recommendations:
  • Quest Nutrition Chocolate Whey-Casein Protein Powder
  • Quest Nutrition Multi-purpose Mix (Unflavored) Whey-Casein Protein Powder
  • Lakanto Semi Sweet Chocolate Chips
    • Use code HAYLSKITCHEN for a discount off your order
  • Lakanto Sugar-free Chocolate Bar
    • Use code HAYLSKITCHEN for a discount off your order
Nutrition:
  • Servings: 14 muffins | Serving size: 1
  • Calories: 102kcal
  • Fat: 2.6g | Saturated fat: 0.8g
  • Carbohydrates: 12.2g | Fiber: 3.3g | Sugar: 1g
  • Protein: 10.1g

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Comments

  1. Nancy Ravault says

    February 03, 2024 at 1:46 pm

    5 stars
    Delicious recipe! I plan to have two as breakfast with my latte. Decadent yet high protein. Didn’t have stevia so used 3 tbsp monkfruit. Was worried it would ruin the recipe but they were good. I’m not a very experienced baker, so wondering how best to store them, as they will last me a week.
    Thank you for your recommendation.
    Nancy

    Reply
    • Haylee Jane Monteiro says

      March 30, 2024 at 1:21 pm

      So glad you liked them. Happy to know the monkfruit sub worked for you.

      They’ll last 3-4 days in the fridge and longer in the freezer.

      Reply

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Hi, I'm Haylee!

I use my passion for baking (and my sweet tooth) to create healthy, high protein, low fat and sugar free desserts and sweet treats that are actually delicious.

Come join me in Hayl's Kitchen and let's eat high protein, sweet and guilt free!

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