Healthy Cinnamon Pumpkin Protein Muffins

I didn’t discover protein muffins until my 30s, and back then, they were always these dry, chalky things that tasted like cardboard. That’s just how they were, I thought – the price you paid for trying to eat healthy.

But then I started playing around with pumpkin in my baking. Turns out, pumpkin puree is like magic when it comes to keeping baked goods moist, and when you add a sprinkle of cinnamon, nobody can tell these muffins are packed with protein. They’re the kind of treat you can feel good about grabbing on busy mornings, and my kids actually ask for them by name.

What Kind of Pumpkin Should I Use?

For these protein muffins, you’ll want to use pure pumpkin puree, not pumpkin pie filling – they’re two very different products that can’t be swapped. The canned pure pumpkin puree (like Libby’s) is your best bet, as it has a consistent texture and moisture content that’s perfect for baking. While you could make your own puree from fresh pumpkin, it tends to be more watery and can throw off the recipe’s texture. If you do go the homemade route, make sure to strain your puree through a cheesecloth to remove excess moisture. Just remember to check the can’s label carefully at the store – pumpkin pie filling looks similar but contains added sugars and spices that would make your muffins too sweet.

Options for Substitutions

These protein-packed muffins are pretty flexible when it comes to ingredients. Here are some handy swaps you can try:

• Whole wheat pastry flour: You can use regular whole wheat flour, all-purpose flour, or even oat flour (though the texture will be slightly denser with oat flour).
• Ground flax seed: Try ground chia seeds instead, or use additional flour plus 2 tablespoons of protein powder for extra protein content.
• Pumpkin pie spice: Make your own by mixing 2 tablespoons cinnamon, 1 teaspoon each of ginger and nutmeg, and 1/2 teaspoon each of cloves and allspice.
• Greek yogurt: Plain yogurt, dairy-free yogurt, or mashed banana can work here. If using banana, reduce the applesauce by 2 tablespoons.
• Coconut sugar: Brown sugar, maple syrup, or honey are good alternatives. If using liquid sweeteners, reduce the applesauce by 1 tablespoon.
• Coconut oil: Any neutral oil works fine here – try avocado oil, light olive oil, or melted butter.
• Pumpkin puree: This is pretty important for the recipe, but in a pinch, you could use mashed sweet potato or butternut squash puree.

Watch Out for These Mistakes While Baking

The biggest challenge when making protein muffins is ending up with dry, dense results – to keep them moist, be careful not to overmix the batter once you combine the wet and dry ingredients, and stir just until everything is incorporated. Using room temperature ingredients (especially the eggs and yogurt) helps create a smoother batter and ensures even baking, so take them out of the fridge 30 minutes before starting. When measuring the flour, avoid packing it into the measuring cup – instead, use the spoon-and-level method by spooning the flour into the cup and leveling it off with a knife. A common timing mistake is overbaking these muffins – since they’re packed with moisture-rich ingredients like pumpkin and applesauce, they’ll continue cooking slightly after you take them out, so remove them when a toothpick comes out with just a few moist crumbs.

What to Serve With Pumpkin Protein Muffins?

These healthy pumpkin muffins make a perfect grab-and-go breakfast or afternoon snack, but there are lots of tasty ways to make them even more filling. Try spreading a warm muffin with a layer of almond or peanut butter, or serve alongside a hot cup of coffee or chai tea for a cozy morning treat. For a more substantial breakfast, pair your muffin with some Greek yogurt topped with honey and chopped nuts, or enjoy with a side of fresh fruit like sliced apples or pears that complement those warm fall spices. If you’re serving these for brunch, they go great with a veggie-packed omelet or frittata for a balanced meal.

Storage Instructions

Counter Storage: These pumpkin protein muffins stay fresh at room temperature for about 2 days. Just keep them in an airtight container lined with paper towels to absorb any excess moisture. They’re perfect for grabbing on your way out the door!

Refrigerate: Pop these muffins in an airtight container and store them in the fridge for up to a week. The paper towel trick works great here too – it helps keep them from getting too moist. They make such an easy grab-and-go breakfast or snack throughout the week.

Freeze: These muffins are fantastic for freezing! Let them cool completely, then wrap them individually in plastic wrap and place in a freezer bag. They’ll stay good for up to 3 months. When you’re ready to eat one, just thaw it overnight in the fridge or pop it in the microwave for about 30 seconds.

Warm Up: Want to enjoy your muffin warm? Just pop it in the microwave for 10-15 seconds. If you like them a bit crispy on top, try splitting them in half and putting them under the broiler for a minute – it makes the cinnamon-sugar topping extra special!

Preparation Time	15-20 minutes
Cooking Time	30-35 minutes
Total Time	45-55 minutes
Level of Difficulty	Medium

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 900-1000
• Protein: 30-35 g
• Fat: 35-40 g
• Carbohydrates: 120-130 g

Ingredients

For the muffin batter:

• 2/3 cup ground flaxseed
• 3/4 cup whole wheat pastry flour
• 1 tsp cinnamon
• 1/2 tsp salt (fine grain)
• 1 tbsp coconut oil (melted and cooled)
• 1 tsp baking soda
• 2 eggs (large)
• 3/4 cup pumpkin puree (I use Libby’s pumpkin puree, ensuring it’s not pie filling)
• 3/4 cup vanilla greek yogurt
• 3 tbsp pumpkin pie spice
• 1 tsp vanilla extract
• 1/2 cup applesauce (unsweetened)

For the cinnamon sugar topping:

• 3 tsp ground cinnamon (freshly ground for best aroma)
• 1/4 cup coconut sugar

Step 1: Preheat the Oven and Prepare Muffin Liners

Preheat your oven to 350 degrees Fahrenheit.

Place 12 silicone muffin liners into a standard muffin tin.

Alternatively, if you are using paper liners, spray them with non-stick cooking spray to prevent your muffins from sticking.

Step 2: Combine Dry Ingredients

• 3/4 cup whole wheat pastry flour or white whole wheat flour
• 2/3 cup finely ground flaxseed
• 3 tbsp pumpkin pie spice
• 1 tsp cinnamon
• 1 tsp baking soda
• 1/2 tsp salt

In a medium-sized bowl, combine the 3/4 cup whole wheat pastry flour or white whole wheat flour, 2/3 cup finely ground flaxseed, 3 tablespoons pumpkin pie spice, 1 teaspoon cinnamon, 1 teaspoon baking soda, and 1/2 teaspoon salt.

Stir these ingredients together until they are evenly mixed, then set the bowl aside.

Step 3: Whisk Together Wet Ingredients

• 2 eggs
• 3/4 cup pure pumpkin puree (unsweetened, not pie filling)
• 3/4 cup vanilla Greek yogurt
• 1/2 cup plain applesauce
• 1 tbsp melted coconut oil
• 1 tsp vanilla extract

In a large bowl, whisk together the 2 eggs, 3/4 cup pure pumpkin puree, 3/4 cup vanilla Greek yogurt, 1/2 cup plain applesauce, 1 tablespoon melted coconut oil, and 1 teaspoon vanilla extract until smooth and well combined.

Step 4: Mix Wet and Dry Ingredients

• Dry ingredient mixture from step 2

Gently fold the dry ingredients into the bowl of wet ingredients until they are just combined.

Be sure not to overmix to keep the muffins light and airy.

Step 5: Fill Muffin Liners with Batter

• Muffin batter from step 4

Scoop the prepared muffin batter evenly into the 12 muffin cups, filling each liner until it is about 7/8 full.

I like to ensure each cup has an even amount to make sure they bake evenly.

Step 6: Prepare and Add Cinnamon Sugar Topping

In a small bowl, mix together 2 tablespoons of coconut sugar and 1/2 teaspoon cinnamon.

Sprinkle this cinnamon sugar mixture evenly over the top of each muffin.

Make sure to use all of the cinnamon sugar for the best flavor.

Step 7: Bake and Cool Muffins

Bake the muffins in the preheated oven for 30-35 minutes, or until a toothpick inserted into the center of a muffin comes out clean.

Allow the muffins to cool in the pan for 15 minutes before serving.

This cooling period helps them firm up and makes them easier to remove from the liners.

Step 8: Serving Tip

I like to enjoy these muffins slightly warm for a comforting breakfast or snack.

To elevate the flavor profile, serve them with a pat of butter or a dollop of your favorite yogurt.