These high-protein pumpkin pie tortillas are a simple, seasonal dessert that tastes indulgent while remaining lighter than a traditional pumpkin pie. Made with Greek yogurt, pumpkin puree, eggs and a flour tortilla crust, each serving delivers about 16 grams of protein, less sugar, and plenty of pumpkin spice flavor. They work well for dessert, a snack, or even a cozy breakfast treat.

This recipe is a quick twist on a yogurt-cheesecake-style filling, baked inside a tortilla to create a shortcut crust. The filling combines high-protein yogurt, canned pumpkin puree, eggs and warming pumpkin pie spice for a creamy, custard-like texture. A touch of tapioca flour or arrowroot firms the filling while keeping it smooth.

Ingredients you’ll need:
This recipe uses just a handful of ingredients—simple staples that keep prep fast and cleanup easy.
- Pumpkin puree: Use 100% pure pumpkin puree for the best flavor. Homemade puree works fine if you prefer.
- Vanilla Greek yogurt: Choose a high-protein vanilla Greek yogurt. If using plain yogurt, add 1 teaspoon vanilla extract to the filling.
- Eggs: Eggs set the filling and create a custardy texture—two large eggs are used in the full batch.
- Pumpkin pie spice: A small amount adds classic autumn warmth; adjust to taste.
- Tapioca flour or arrowroot: A tablespoon helps firm the filling without changing flavor.
- Maple syrup: Natural sweetener; substitute a zero-calorie sweetener if you prefer lower sugar.
- Tortillas: Regular flour tortillas form the tart shells. Use gluten-free or grain-free tortillas if needed.

How to make protein pumpkin pie tortillas
These mini pies come together quickly. Read through the steps before starting so you can work confidently at the right temperatures and timing.
1. Preheat: Heat the oven to 160°C / 350°F.
2. Make the filling: In a medium bowl, whisk together the Greek yogurt, pumpkin puree, eggs, maple syrup, pumpkin pie spice and tapioca flour until smooth and runny, like a custard.
3. Form the shells: Lightly press tortillas into small round ramekins to shape a shallow cup that will hold the filling. Fresh tortillas are easier to shape.
4. Fill: Divide the pumpkin custard between the tortilla shells, pouring slowly so each cup receives an even amount.
5. Bake: Place the filled ramekins on a baking tray and bake 30–40 minutes, or until the filling is set and slightly caramelized at the edges. If the tortilla edges brown too quickly, tent the tops loosely with foil for the last part of baking.
6. Cool and serve: Allow the mini pies to cool for about 20 minutes before removing from the ramekins. Serve warm or chilled with a dollop of whipped cream or a spoonful of vanilla yogurt.

Tips on making pumpkin tortillas
- Use fresh, soft tortillas so they bend easily into the ramekins without cracking.
- The full filling recipe makes two decent-sized pies. Scale down by half for a single serving or multiply for a crowd.
- Whisk the filling thoroughly until smooth; this prevents lumps and ensures a silky texture.
- Oven strength varies—start checking for set after 25–30 minutes to avoid overbaking.
- The pies are done when the center is set and the edges show a little color.

How to store homemade healthy pumpkin pie
Once cooled, place the pies in an airtight container lined with a paper towel to absorb any excess moisture. Store in the refrigerator for up to five days. Enjoy straight from the fridge or briefly warmed—top with whipped cream or a spoonful of yogurt when serving.

FAQs
Can I make this dairy free?
You can try a thick, high-protein plant-based yogurt in place of Greek yogurt, but results may vary because dairy-free yogurts behave differently during baking. If you attempt a substitute, choose a very thick yogurt and reduce any extra liquid in the filling.
Can I make them sweeter?
Yes. Using a sweetened vanilla Greek yogurt and the maple syrup in the recipe usually provides pleasant sweetness. For less sugar, substitute a low-calorie sweetener such as monk fruit or liquid stevia to taste.
Can you freeze protein pumpkin pie tortillas?
Freezing is not recommended for the best texture. The tortilla crust can become soggy after thawing. These pies are best enjoyed fresh or refrigerated for a few days.

Other pumpkin dessert ideas
If you enjoy these mini pumpkin pies, try experimenting with other pumpkin desserts like baked pumpkin oatmeal, pumpkin mug cake, or gluten-free pumpkin donuts. All of these capture pumpkin’s warming spice and pair well with a swirl of cream or yogurt.
If you try this pumpkin pie tortilla recipe, feel free to leave a comment with your feedback or any variations you experimented with. It’s a forgiving recipe that adapts well to swaps and scaling.
High Protein Pumpkin Pie Tortillas
- Author: Caitlin Rule
- Total Time: 45 minutes
- Yield: Makes 2
Ingredients
- ⅔ cup (80g) vanilla Greek yogurt
- ¼ cup (60g) pumpkin puree (unsweetened)
- 2 large eggs
- 1 ½ tablespoons maple syrup
- ½ teaspoon pumpkin pie spice
- 1 tablespoon tapioca flour or arrowroot starch
- 2 regular flour tortillas (or gluten-free alternatives)
- Optional: whipped cream or extra yogurt to serve
Instructions
- Preheat your oven to 350°F / 160°C.
- Whisk the yogurt, pumpkin, eggs, maple syrup, pumpkin spice and tapioca flour in a medium bowl until smooth and custard-like.
- Press tortillas into small round ramekins to form cups for the filling.
- Pour the filling into the tortilla shells and bake 30–40 minutes until set. Tent with foil if the edges brown too quickly.
- Cool for about 20 minutes before serving. Serve warm or chilled with whipped cream or vanilla yogurt.
Notes
- Store finished pies in an airtight container in the refrigerator for up to five days.
- Prep Time: 10 minutes
- Cook Time: 35 minutes
- Category: Dessert, Holidays
- Method: Bake
- Cuisine: American
Nutrition
- Serving Size: 1 pie
- Calories: 243
- Sugar: 16.1g
- Fat: 62g
- Carbohydrates: 30.4g
- Protein: 16.1g