Start by preheating your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or spray it generously with non-stick cooking spray to ensure the muffins release easily after baking.
In a large mixing bowl, whisk together the oat flour, vanilla protein powder, sweetener, baking powder, baking soda, salt, and poppy seeds. Make sure there are no large clumps of protein powder so the texture remains consistent.
In a separate medium bowl, beat the eggs lightly. Add the Greek yogurt, almond milk, fresh lemon juice, lemon zest, and vanilla extract. Whisk until the mixture is smooth and the yogurt is fully incorporated.
Pour the wet ingredients into the bowl with the dry ingredients. Use a spatula to gently fold the mixture together until just combined. Be careful not to overmix, as this can make the protein muffins tough and gummy.
Divide the batter evenly among the 12 muffin cups. Each cup should be about three-quarters full. If you have extra poppy seeds, you can sprinkle a tiny bit more on top for a professional look.
Place the tin in the center of the oven and bake for 18 to 20 minutes. You can check for doneness by inserting a toothpick into the center of a muffin; it should come out clean or with just a few moist crumbs. Let the muffins cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.