Healthy Pumpkin Spice Protein Bagels

Here are my pumpkin spice protein bagels, with Greek yogurt and pumpkin puree for moisture, a blend of flours and flaxseed for extra protein and fiber, warm fall spices, and sweet raisins throughout.

These bagels have become my go-to breakfast during pumpkin season. I love making a batch on Sunday and freezing half so we have an easy, filling breakfast all week long. They’re way better than store-bought bagels, and honestly, they make the whole house smell amazing.

What Kind of Pumpkin Puree Should I Use?

For this recipe, you’ll want to grab plain canned pumpkin puree from the baking aisle, not pumpkin pie filling which already has sugar and spices added. Both organic and regular brands work just fine, so pick whichever fits your budget. If you’re using fresh pumpkin puree, make sure to drain any excess liquid by placing it in a fine-mesh strainer for about 15 minutes before measuring it out. The key is to avoid a watery puree that could make your bagels too dense or soggy, so look for a thick, smooth consistency that holds its shape when you scoop it.

Options for Substitutions

These bagels are pretty forgiving when it comes to swaps, so here are some options if you need them:

• Greek yogurt: Regular plain yogurt works fine, though Greek yogurt gives a better texture. You can also use sour cream or even mashed banana if you’re in a pinch, though the flavor will be slightly different.
• Pumpkin puree: Make sure you’re using pure pumpkin puree and not pumpkin pie filling. If you don’t have pumpkin, try mashed sweet potato or butternut squash – you’ll get a similar texture and color.
• Wheat flour: You can use all-purpose flour instead of wheat flour if that’s what you have. The bagels will be a bit lighter in texture and color.
• Flaxseed meal: Chia seeds or wheat germ make good substitutes. You can also just add an extra 2 tablespoons of flour if you don’t have any of these on hand.
• Pumpkin pie spice: Don’t have the pre-mixed spice? Mix together 1 teaspoon cinnamon, 1/2 teaspoon ginger, 1/4 teaspoon nutmeg, and 1/4 teaspoon cloves.
• Raisins: Swap these with dried cranberries, chopped dates, or chocolate chips. You can also leave them out completely if you prefer plain bagels.
• Honey: Maple syrup or agave nectar work just as well for sweetness.

Watch Out for These Mistakes While Baking

The biggest mistake when making these bagels is adding too much flour during kneading, which can make them dense and dry – the dough should feel slightly sticky but manageable, so resist the urge to keep flouring your hands and work surface.

Another common error is skipping the egg wash, which not only gives bagels that golden-brown color but also helps create a slightly firmer outer layer that makes them feel more like real bagels.

Make sure your baking powder is fresh (test it by dropping a pinch in hot water – it should fizz), since expired leavening will result in flat, hockey-puck-like bagels instead of ones with a nice rise.

When shaping the ropes, seal the ends together firmly by overlapping them and pinching well, otherwise they’ll come apart during baking and you’ll end up with crescent rolls instead of bagels.

What to Serve With Pumpkin Spice Protein Bagels?

These bagels are perfect for breakfast or a post-workout snack, and they taste amazing with a good schmear of cream cheese – try mixing in a little cinnamon or maple syrup for extra fall flavor. I love toasting mine and spreading on some almond butter or peanut butter, which adds protein and pairs really well with the pumpkin and spices. If you want something lighter, a thin layer of ricotta cheese with a drizzle of honey is delicious and keeps things from getting too heavy. These bagels also work great alongside your morning coffee or as an afternoon pick-me-up with a cup of chai tea.

Storage Instructions

Store: Keep your pumpkin spice bagels in an airtight container or zip-top bag at room temperature for up to 3 days. If you want them to last longer, store them in the fridge for up to a week—they’ll stay fresh and ready to toast whenever you need a quick breakfast.

Freeze: These bagels are perfect for freezing! Let them cool completely, then wrap each one individually in plastic wrap before placing them all in a freezer bag. They’ll keep for up to 3 months, which is great for meal prep.

Toast: To enjoy a frozen bagel, you can either let it thaw on the counter for about 30 minutes or pop it straight into the toaster from frozen. I usually slice mine in half before freezing so they toast up nice and crispy without any extra wait time.

Estimated Nutrition

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

• Calories: 1300-1450
• Protein: 38-46 g
• Fat: 16-22 g
• Carbohydrates: 270-295 g

Ingredients

For the dough:

• 1 cup greek yogurt (I prefer Fage for its thick consistency)
• 3/4 cup pumpkin puree (I use Libby’s for the best color and texture)
• 2 tbsp honey
• 1 1/2 cups flour (I always use King Arthur all-purpose flour)
• 1 cup wheat flour
• 2 tbsp flaxseed meal
• 1 tbsp baking powder
• 2 1/2 tsp pumpkin pie spice
• 1 1/2 tsp cinnamon
• 3/4 tsp salt
• 1/2 cup raisins
• 1/2 tsp vanilla extract

For the topping:

• 1 egg (beaten with 1 tsp water for a glossier finish)

Step 1: Prepare Your Workspace and Preheat

Preheat your oven to 375°F and line a large baking sheet with parchment paper.

This gives you time to prepare your ingredients while the oven reaches temperature.

Having everything ready before you start mixing ensures a smooth, uninterrupted workflow.

Step 2: Combine Wet Ingredients

• 1 cup Greek yogurt
• 3/4 cup pumpkin puree
• 2 tbsp honey

In a large mixing bowl, combine the Greek yogurt, pumpkin puree, and honey, stirring until well blended and smooth.

The yogurt provides the protein structure while the pumpkin adds moisture and flavor—mixing these first creates your flavor and texture base before adding the dry ingredients.

I prefer Fage yogurt because its thickness creates a better dough consistency that holds together beautifully during shaping.

Step 3: Mix Dry Ingredients and Combine

• 1 1/2 cups all-purpose flour
• 1 cup wheat flour
• 2 tbsp flaxseed meal
• 1 tbsp baking powder
• 2 1/2 tsp pumpkin pie spice
• 1 1/2 tsp cinnamon
• 3/4 tsp salt
• 1/2 cup raisins
• 1/2 tsp vanilla extract
• wet ingredient mixture from Step 2

In a separate bowl, whisk together the all-purpose flour, wheat flour, flaxseed meal, baking powder, pumpkin pie spice, cinnamon, and salt.

Pour this dry mixture into the wet ingredients from Step 2, then fold in the raisins and vanilla extract.

Stir until just combined—be careful not to overmix, as this can lead to dense bagels.

I like to add the raisins last and fold them in gently so they distribute evenly without breaking apart.

Step 4: Knead and Shape the Dough

• dough mixture from Step 3

Turn the dough out onto a lightly floured surface and knead by hand for about 1-2 minutes until it becomes smooth and slightly elastic—this develops the structure without overworking it.

Divide the dough into 8 equal portions by rolling it into a rope and cutting sections, then roll each portion into a ball.

Take each ball and roll it into a 7-inch rope, then bring the ends together and press firmly to form a bagel shape with a small hole in the center.

Place each bagel on your prepared baking sheet with even spacing.

Step 5: Apply Egg Wash and Bake

• 1 egg
• shaped bagels from Step 4

In a small bowl, beat the egg with 1 teaspoon of water until combined.

Brush this egg wash over the top and sides of each bagel for a glossy, golden finish.

Bake in your preheated 375°F oven for 20-25 minutes, until the bagels are golden brown and firm to the touch.

They should feel set on the outside but still have a slight give when pressed gently.

Step 6: Cool and Serve

• baked bagels from Step 5

Remove the bagels from the oven and let them cool on the baking sheet for 10-15 minutes before transferring to a wire rack or serving.

This cooling period allows the structure to set properly so they hold their shape beautifully.

Once cooled, slice and toast if desired, or serve as-is with cream cheese, butter, or your favorite topping.

Healthy Pumpkin Spice Protein Bagels

Delicious Healthy Pumpkin Spice Protein Bagels recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 20 minutes mins

Cook Time 35 minutes mins

Total Time 57 minutes mins

Servings 8 bagels

Calories 1375 kcal

Ingredients

  

For the dough

• 1 cup greek yogurt (I prefer Fage for its thick consistency)
• 3/4 cup pumpkin puree (I use Libby's for the best color and texture)
• 2 tbsp honey
• 1 1/2 cups flour (I always use King Arthur all-purpose flour)
• 1 cup wheat flour
• 2 tbsp flaxseed meal
• 1 tbsp baking powder
• 2 1/2 tsp pumpkin pie spice
• 1 1/2 tsp cinnamon
• 3/4 tsp salt
• 1/2 cup raisins
• 1/2 tsp vanilla extract

For the topping

• 1 egg (beaten with 1 tsp water for a glossier finish)

Instructions

 

• Preheat your oven to 375°F and line a large baking sheet with parchment paper. This gives you time to prepare your ingredients while the oven reaches temperature. Having everything ready before you start mixing ensures a smooth, uninterrupted workflow.
• In a large mixing bowl, combine the Greek yogurt, pumpkin puree, and honey, stirring until well blended and smooth. The yogurt provides the protein structure while the pumpkin adds moisture and flavor—mixing these first creates your flavor and texture base before adding the dry ingredients. I prefer Fage yogurt because its thickness creates a better dough consistency that holds together beautifully during shaping.
• In a separate bowl, whisk together the all-purpose flour, wheat flour, flaxseed meal, baking powder, pumpkin pie spice, cinnamon, and salt. Pour this dry mixture into the wet ingredients from Step 2, then fold in the raisins and vanilla extract. Stir until just combined—be careful not to overmix, as this can lead to dense bagels. I like to add the raisins last and fold them in gently so they distribute evenly without breaking apart.
• Turn the dough out onto a lightly floured surface and knead by hand for about 1-2 minutes until it becomes smooth and slightly elastic—this develops the structure without overworking it. Divide the dough into 8 equal portions by rolling it into a rope and cutting sections, then roll each portion into a ball. Take each ball and roll it into a 7-inch rope, then bring the ends together and press firmly to form a bagel shape with a small hole in the center. Place each bagel on your prepared baking sheet with even spacing.
• In a small bowl, beat the egg with 1 teaspoon of water until combined. Brush this egg wash over the top and sides of each bagel for a glossy, golden finish. Bake in your preheated 375°F oven for 20-25 minutes, until the bagels are golden brown and firm to the touch. They should feel set on the outside but still have a slight give when pressed gently.
• Remove the bagels from the oven and let them cool on the baking sheet for 10-15 minutes before transferring to a wire rack or serving. This cooling period allows the structure to set properly so they hold their shape beautifully. Once cooled, slice and toast if desired, or serve as-is with cream cheese, butter, or your favorite topping.