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These Gluten Free Pumpkin Muffins are moist, fluffy, and packed with cozy pumpkin flavor, all while being high in protein. They’re perfect for anyone looking for a tasty treat that feels a little indulgent but is still wholesome and gluten free. You’ll notice a lovely spice mix with cinnamon and nutmeg that makes these muffins smell like fall in every bite.

I love making these muffins for a quick breakfast or an afternoon snack. They’re easy to whip up and stay good for a few days, which is great when I’m busy but still want something nutritious on hand. Using a mix of almond flour and protein powder gives them a nice boost, so I feel good about grabbing one before heading out the door.

My favorite way to eat these pumpkin muffins is with a little smear of cream cheese or nut butter on top. It adds just a bit of extra creaminess and makes the snack feel a little more special. Whether you’re feeding kids, meal prepping, or just craving something soft and warm, these muffins hit the spot every time!

Key Ingredients & Substitutions

Pumpkin Puree: Use canned or fresh pumpkin. Make sure it’s pure pumpkin, not pumpkin pie filling with added sugar. If unavailable, sweet potato makes a good substitute with similar moisture and flavor.

Almond Flour: This adds moisture and a tender texture. If allergic to nuts, swap it with more oat flour or gluten-free all-purpose flour, but note the texture may be slightly different.

Protein Powder: Choose vanilla or unflavored whey or plant-based protein powder. Pea or rice protein works well for plant-based diets. If avoiding protein powder, add a little extra almond flour to keep texture.

Chocolate Chips: Optional but adds sweetness and texture. Use dairy-free chips for a vegan option or skip them altogether for a simpler muffin.

How Do I Make Sure My Muffins Stay Moist and Fluffy?

Moisture and fluffiness in gluten-free muffins can be tricky but here’s how to get it right:

• Don’t overmix the batter. Mix just until ingredients are combined to prevent dense muffins.
• Use a mix of almond flour and oat flour for balance – almond flour adds moisture, oat flour gives structure.
• Let the batter rest a few minutes before baking to let the flours absorb moisture.
• Bake at 350°F and check with a toothpick after 20 minutes to avoid overbaking, which dries muffins out.
• Cool muffins in the pan briefly to set them, then move to a rack to keep the texture soft.

Equipment You’ll Need

• Standard muffin tin – I use this because it helps the muffins bake evenly and holds their shape well.
• Mixing bowls – one for wet ingredients, another for dry, to keep things organized and easy to combine.
• Whisk – helpful for blending the pumpkin, eggs, and liquids smoothly.
• Spoon or spatula – for gently folding the dry ingredients into the wet without overmixing.
• Measuring cups and spoons – ensures the ingredients are just right for perfect muffins.
• Cooling rack – to cool the muffins completely, keeping their tops soft and preventing sogginess.

Flavor Variations & Add-Ins

• Swap chocolate chips for chopped nuts like pecans or walnuts for extra crunch and flavor.
• Mix in dried cranberries or raisins for a touch of tart sweetness and texture.
• Add a swirl of almond or peanut butter into the batter before baking for an extra rich flavor.
• Use pumpkin spice or add a pinch of ground ginger and cloves for a more fall-inspired taste.

Gluten Free Pumpkin Muffins (High Protein)

Ingredients You’ll Need:

• 1 cup pumpkin puree (canned or fresh)
• 1 cup almond flour
• 1/2 cup gluten-free oat flour (or gluten-free all-purpose flour)
• 1/2 cup vanilla or unflavored protein powder (whey or plant-based)
• 1/4 cup coconut sugar or brown sugar
• 1/4 cup maple syrup or honey
• 2 large eggs
• 1/4 cup unsweetened almond milk (or any milk)
• 2 tsp pumpkin pie spice (or 1 tsp cinnamon + 1/2 tsp nutmeg + pinch of cloves)
• 1 tsp baking powder (gluten-free)
• 1/2 tsp baking soda
• 1/4 tsp salt
• 1 tsp vanilla extract
• 1/4 cup mini dairy-free or regular chocolate chips (optional, plus extra for topping)

How Much Time Will You Need?

It takes about 10 minutes to prepare the batter and 20–25 minutes to bake the muffins. Then allow about 10 minutes for cooling before serving. So overall, you’re looking at around 40–45 minutes from start to finish.

Step-by-Step Instructions:

1. Prepare for Baking:

Preheat your oven to 350°F (175°C). Line a muffin tin with 8 paper liners to keep the muffins from sticking and help them bake evenly.

2. Mix Wet Ingredients:

In a large bowl, whisk together the pumpkin puree, eggs, maple syrup or honey, almond milk, and vanilla extract until everything is smooth and creamy.

3. Combine Dry Ingredients:

In another bowl, mix the almond flour, gluten-free oat flour, protein powder, coconut sugar, pumpkin pie spice, baking powder, baking soda, and salt until evenly combined.

4. Make the Batter:

Gently fold the dry ingredients into the wet ingredients, stirring just until everything is blended – be careful not to overmix or the muffins may turn dense. Fold in the chocolate chips if using.

5. Fill Muffin Cups and Bake:

Divide the batter evenly among the 8 muffin liners. Sprinkle a few chocolate chips on top of each muffin for extra melty goodness. Bake in the preheated oven for 20–25 minutes. Check doneness by inserting a toothpick into the center—it should come out clean.

6. Cool and Enjoy:

Let the muffins cool in the pan for about 10 minutes, then transfer them to a wire rack to cool completely. Enjoy warm or at room temperature! Store any leftovers in an airtight container for up to 4 days or freeze for longer storage.

Can I Use Frozen Pumpkin Puree for These Muffins?

Yes! Just make sure to thaw it fully and drain any excess liquid if needed before using, so your batter doesn’t get too watery.

Can I Substitute the Almond Flour?

Absolutely. You can replace almond flour with more oat flour or a gluten-free all-purpose flour blend, but note that the texture may be a bit less moist without the almond flour’s natural oils.

How Should I Store Leftover Muffins?

Keep leftovers in an airtight container at room temperature for up to 2 days or in the fridge for up to 4 days. To freeze, wrap each muffin individually and store them in a freezer-safe bag for up to 3 months.

Is There a Vegan Option for This Recipe?

You can try swapping the eggs with flax eggs (1 tbsp ground flaxseed mixed with 3 tbsp water per egg) and use a plant-based protein powder and chocolate chips to keep it vegan—results may vary slightly in texture.