Easy Low Carb Pumpkin Protein Muffins (Healthy & Moist!)

This low carb pumpkin protein muffin recipe creates incredibly moist, warmly spiced treats that are packed with protein for a truly satisfying bite. I find these muffins perfect when I need a quick, healthy breakfast or a tasty pick-me-up that reminds me of cozy fall days. They are wonderfully easy to whip up using just a few simple ingredients and minimal cleanup.

A plate of golden pumpkin protein muffins, showcasing their warm spices and inviting appearance.

What Ingredients You’ll Need for These Protein-Packed Pumpkin Muffins

Like I mentioned earlier, you only need a handful of items from your pantry for this recipe. Let’s quickly go over the main players and touch on a few common questions you might have about swapping things out.

Almond Flour

This is one of the two primary ingredients giving these muffins their structure. Because it plays such a big role, it is a bit tricky to substitute directly. You could potentially try using other low carb flour options, like coconut flour, but be aware that coconut has a distinct flavor that might be difficult to hide.

Close-up of golden pumpkin protein muffins with a soft, slightly cracked top, ready to be enjoyed.

If you need to avoid almond flour completely, perhaps due to an allergy, you might consider using regular all purpose flour. Another option could be something similar to the graham cracker crumbs I have used in other protein muffin recipes I have developed. When trying these other flours, I would suggest starting with the same amount by weight and then adjusting as needed to get the right batter consistency. I always like to have a visual idea of how the batter should look before baking for comparison.

Golden pumpkin protein muffins topped with a glossy glaze, adding a touch of sweetness to their earthy tones.

Protein Powder

The second key ingredient for structure is your protein powder. I often use a blend that combines whey and casein protein because it tends to be a little thicker than just a whey-only powder. If your protein powder is different, you might need to make small adjustments to the liquid amount to get the batter just right.

When I first worked on this recipe, I actually used a pumpkin spice flavored whey concentrate. I ended up using a bit more of that protein powder and less of the canned pumpkin puree compared to this current version. You can get a good sense of how the batter should feel and look from seeing it before it goes into the oven. As long as your batter is reasonably close in consistency, your protein muffins should turn out just fine.

Golden-brown low carb pumpkin protein muffins arranged on a white surface, showcasing their moist texture and warm spices.

Wet Ingredients

For the wet part of the batter, you only need canned pumpkin and eggs. It is wonderfully simple. The only potential substitution I can really think of here would be if you had an egg allergy or were using a vegan protein powder that required ditching the eggs.

In that situation, you could likely get away with using extra canned pumpkin. Maybe add a little bit of unsweetened apple sauce too to help replace the moisture and binding that the eggs provide (which is usually around 150 to 200 grams in a recipe like this). It might take a little trial and error.

A Few Closing Thoughts on Making These Low Carb Pumpkin Muffins

In the recipe notes section, I have included a link to where you can find silicone baking cups like the ones I love to use. Honestly, I cannot recommend these enough for baking muffins. Nothing seems to stick to them, which means you do not lose any of that precious batter stuck to the side of paper liners or left behind in the muffin tin. It is a small thing but makes a big difference in cleanup and getting every bit of that delicious muffin.

A plate of golden pumpkin protein muffins dusted with powdered sugar, highlighting their homemade appeal.

Frequently Asked Questions About Pumpkin Protein Muffins

Here are some common questions people ask about making these healthy pumpkin muffins.

Can I use fresh pumpkin puree instead of canned?

Yes, you can use fresh pumpkin puree if you prefer. Just make sure it is well drained to avoid adding too much moisture to the batter, which could affect the muffin texture. Canned puree is often more consistent.

What kind of protein powder works best?

A blend of whey and casein or a good quality whey concentrate usually works well. The absorption rate and thickness can vary between types, so you might need minor adjustments to the liquid or flour to get the right batter consistency. Plant based protein powders can sometimes be used, but results may vary.

How should I store these muffins?

You should store these low carb pumpkin protein muffins in an airtight container at room temperature for a few days. If you need to keep them longer, storing them in the refrigerator can extend their freshness for about a week.

Can I freeze these muffins?

Absolutely. These muffins freeze very well. Once they are completely cool, wrap each muffin individually in plastic wrap and then place them in a freezer safe bag or container. They should keep in the freezer for up to three months. Just thaw them at room temperature or gently warm them up before eating.

Can I add mix-ins like nuts or chocolate chips?

Yes, you can definitely add mix-ins. Things like chopped pecans, walnuts, or sugar free chocolate chips would be delicious additions. Fold them gently into the batter just before spooning it into the muffin cups.

Why did my muffins turn out dense?

Muffins can become dense if the batter is overmixed after the wet and dry ingredients are combined. Make sure you only mix until the ingredients are just combined and there are no dry streaks remaining. Overmixing can develop the gluten in the flour (even almond flour has some) and make the texture tough or dense. Using the correct amount of leavening agent (baking powder) is also important for a light texture.

Are these muffins suitable for meal prepping?

Yes, these pumpkin protein muffins are excellent for meal prepping. Their high protein content makes them a satisfying option for a quick breakfast or snack throughout the week. They store well and are easy to grab on the go.