Pumpkin Protein Muffins

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These pumpkin protein muffins are a delicious, protein packed treat that are also low in sugar and carbs. They hit the spot when you’re craving baked goods, but want to stay on track with your nutritional goals. Feel free to indulge, as these come in at just 160 calories per muffin.

Freshly baked pumpkin protein muffins in a muffin tin. On a cooling rack with a pink dish cloth in the background.

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Why should you try this recipe?
Ingredients
Recipe Variations
Instructions
Equipment
FAQs
How To Serve
Similar Recipes
Pumpkin Protein Muffins

Why should you try this recipe?

Here's why you'll love these pumpkin protein muffins:

They’re easy to make: Made with ingredients and appliances you probably already have in your kitchen. All you need to make these pumpkin protein muffins is a hand mixer, muffin tin, 13 ingredients and 25 minutes.
They’re packed with protein: That’s thanks to the protein powder, greek yogurt, eggs and almond flour. It also makes these muffins the perfect fuel to start the day, power your workout, or pack for on-the-go healthy snacks.
They have a great macro breakdown: It’s not just protein that these muffins are packed with. They have a healthy dose of complex carbs, fibre and healthy fat as well. All crucial macro and micronutrients that help your body operate at it’s best.
They’re a delicious, healthier alternative to traditional baked goods: There’s nothing wrong with indulging in the occasional coffee shop muffin. But, these protein muffins are a lightened up version that are not only loaded with nutrients, but are also much lower in sugar since they’re sweetened naturally. That means you won’t get a blood sugar crash that leaves you feeling sluggish immediately after eating one.

Scroll down to see the printable recipe with nutritional information.

Ingredients

Here's what you'll need for the best protein powder pumpkin muffins.

Almond flour: A popular low-carb alternative to wheat flour. It also adds texture and flavour to the muffins.
Pumpkin puree: Be sure to buy a can of pumpkin puree, not pumpkin pie mix. The first is 100% pumpkin, the second is a sugary mix used to make homemade pumpkin pie.
Banana: Mashed bananas are used as a substitute for fat in baking recipes. They’re also a natural sweetener. That means we can cut back on calories, fat and sugar.
Maple syrup: I replace refined sugars with natural sugars in all of my recipes. While they are still sugar, they are a better option because they have a lower glycemic index and offer up some vitamins and minerals. That means your blood sugar rises more slowly after consuming them and you'll avoid that dreaded post-sugar crash. Be sure to choose 100% pure maple syrup. If you don’t have this in your cupboard, feel free to substitute with one of these sweeteners.
Greek yogurt: Its creaminess helps baked goods retain moisture. Don’t skimp on this or you’ll have dry, flaky muffins instead.
Eggs: This adds structure and stickiness, binding the ingredients in your muffins together. Feel free to replace with a vegan egg substitute if need be.
Protein Powder: You can use whey or plant-based protein powder. I prefer a chocolate flavor, but any flavor will work.
Spices: Cinnamon brings the sweet and spicy, nutmeg brings the pungency, and pumpkin spice brings the…. pumpkin.
Vanilla Extract: Adds a subtle, delicious flavour of vanilla to the muffin.
Salt: Enhances the flavour of all your other ingredients.
Lily's Dark Chocolate Chips: These keto chocolate chips are sweetened with stevia, meaning they are refined-sugar free. I use these to keep the sugar content in these cookies low. However, these can be replaced with any other chocolate chips.

Scroll down to find the printable recipe with ingredient measurements.

Recipe Variations

Make these low carb protein muffins dairy free: Replace the Greek yogurt with a non-dairy yogurt like coconut yogurt. You’ll also need to ensure you’re using a plant-based protein powder instead of whey.
Make these muffins vegan: In addition to the swaps above, you’ll need to use a vegan egg substitute. You can find great options here.
Change the mix-Ins: If you're not a chocolate chip fan, you're crazy. But, I still got your back. Replace the chocolate chips with raisins, walnuts, pecans, or any other dried fruit. Replace with a quantity that suits your taste bud.
Turn up the flavour: If you're looking to turn up the flavour, consider adding cardamom, ginger or cloves, which all pair well with the spices used in this recipe.

Instructions

These pumpkin protein muffins are prepared with a hand mixer in a few easy steps.

Wet ingredients needed for protein pumpkin muffins in a glass mixing bowl on a white counter top.

Dry ingredients needed for protein pumpkin muffins in a glass mixing bowl on a white counter top.

Preheat the oven to 375 degrees F.
Add wet ingredients to a mixing bowl and use a hand mixer to combine.
Add dry ingredients to a mixing bowl and stir. Leave chocolate chips aside.

All ingredients needed for protein pumpkin muffins in a glass mixing bowl on a white counter top.

Wet ingredients needed for protein pumpkin muffins in a glass mixing bowl on a white counter top. Lots of chocolate chips scattered across top.

Make a well in the dry mixing bowl, then pour wet ingredients inside. Use a hand mixer to combine all ingredients. As a general rule of thumb, you don’t want to over mix batter that contains almond flour.
Once mixed, add in ½ cup of chocolate chips and stir with a large spoon.

Muffin tin filled with protein muffin batter. Topped with chocolate chips. Ready to be baked.

Line a muffin tin with muffin liners. Silicone muffin liners are useful because they’re reusable, non-stick, and easily cleaned. But, any muffin liner will work.
Add the batter into the muffin tin cups. Each should be filled ¾ of the way.
Sprinkle remaining chocolate chips on top of the muffins.

Freshly baked pumpkin protein muffins. On a pottery plate with a pink dish cloth surrounding it. Countertop is scattered with chocolate chips.

Bake at 375 for 25 minutes or until a toothpick comes out clean. The tops of the muffins will be golden brown. Note that almond flour burns easier than wheat flour, so be sure to keep an eye on the muffins in the remaining minutes.
Remove from the oven and let cool completely before eating.

Recipe Notes

Let cool completely before serving. The cohesiveness of low-carb baked goods improves after being cooled. So, please resist digging into the muffins too soon or you'll end up with a pile of crumbs.
Remember, pumpkin puree and pumpkin pie mix are different. You will find both canned pumpkin puree and pumpkin pie mix near the baking aisle. The mix is actually a pre-made pumpkin pie filling that's loaded with sugar. The puree is generally labeled "organic pumpkin" or "100% pure pumpkin."
Note that almond flour burns easier than wheat flour, so be sure to keep an eye on the muffins in the remaining minutes.

How To Store

How to store: Store in an airtight container on the counter for up to 5 days or in the refrigerator for up to 7 days.
How to freeze: If you need to store for longer, you can freeze them. Be sure to let the muffins cool completely before adding to an airtight container or Ziploc freezer bag.
How to reheat: Warm in the microwave for 30 seconds. You can also reheat in the oven by baking at 350 for 10 minutes.

For the full ingredient list and step-by-step directions, scroll down to view the recipe card.

Equipment

Here's what you need to make this pumpkin protein muffins recipe.

Hand Mixer: A necessary tool to ensure ingredients are fully mixed together.
Muffin tray: Needed to get that classic muffin shape.
Cookie Scoop: This isn't a necessity, but works great to transfer batter to the muffin tray and guarantee evenly sized muffins.
Silicone muffin liners: I use silicone muffin liners because muffins are very easy to pop out after they cool. These are also great because they’re reusable and easy to clean.

FAQs

Here are some of the most frequently asked questions about this low carb protein muffin recipe.

Is canned pumpkin the same as pumpkin puree?

Yes, these terms are used interchangeably in recipes. Both are 100% steamed and pureed pumpkin.

Which protein powder is best for baking?

Whey, soy and pea protein can be used in baking. The whey protein has a moist, cake-like texture that I personally prefer in baked goods. But, all will result in moist, delicious muffins.

How To Serve

Now that you have these delicious, protein powder pumpkin muffins, it’s time to build the perfect meal with them. Here’s a few delicious options.

Pairing the muffin with a warming drink like my creamy matcha chai latte.
Adding a little “icing”. My favourite healthy icing ideas are drizzling almond butter, coconut yogurt or healthy whip cream on top of the muffin. You can find my homemade almond butter recipe here.

Similar Recipes

Still hungry? If you enjoyed this recipe for pumpkin protein muffins, I invite you to check out my collection of other healthy desserts or check out the pumpkin recipes I hand selected for you below.

If you make these protein pumpkin muffins, please consider leaving a star rating and a comment. Don't forget to tag @caiteyjay on Instagram or @caiteyjay on Pinterest so I can see your creations.