Preheat your oven to 350°F (175°C). This ensures that the muffins bake evenly and rise properly.

Grease a muffin tin with cooking spray or line it with muffin liners to prevent sticking.

In a large mixing bowl, combine the whole wheat flour, rolled oats, baking powder, baking soda, cinnamon, nutmeg, salt, and protein powder. Whisk together until well combined. This helps to evenly distribute the leavening agents and spices.

In another bowl, mix together the pumpkin puree, Greek yogurt, honey, eggs, almond milk, and vanilla extract. Whisk until smooth. This step is crucial for incorporating air into the mixture, which helps the muffins rise.

Pour the wet ingredients into the dry ingredients. Using a rubber spatula, gently fold the mixture together until just combined. Be careful not to overmix, as this can lead to dense muffins.

Scoop the batter into the prepared muffin tin, filling each cup about ⅔ full. This allows room for the muffins to rise.

Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean. This indicates that the muffins are fully cooked.

Remove the muffins from the oven and let them cool in the tin for 5 minutes. Then transfer them to a wire rack to cool completely. This helps maintain their texture and prevents sogginess.

Enjoy your high protein pumpkin muffins warm or at room temperature. They can be stored in an airtight container for up to 5 days.