Prep the pan and oven: Heat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease.
Whisk the dry ingredients: In a large bowl, whisk 1 cup whole wheat pastry flour, 1 cup almond flour, 1 tablespoon baking powder, 1/4 teaspoon baking soda, and 1/2 teaspoon salt.
Mix the wet ingredients: In a separate bowl, whisk 2 large eggs, 1/2 cup granulated allulose (or erythritol/monk fruit blend), 3/4 cup plain Greek yogurt, 1/3 cup milk, 1/4 cup oil (or melted butter), 1 1/2 teaspoons vanilla, and optional zest of 1 lemon until smooth.
Combine gently: Pour wet into dry. Stir with a spatula just until no big dry patches remain. The batter will be thick.
Fold in berries: Add 1 1/2 cups blueberries. If using frozen, toss them in 1 teaspoon of the flour first to reduce streaking. Fold gently to avoid smashing.
Portion: Divide batter evenly among muffin cups, filling about 3/4 full. Sprinkle a few extra berries on top if you like.
Bake: Bake 18–22 minutes, or until the tops are set, lightly golden at the edges, and a toothpick comes out with a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then move to a rack to finish cooling. Sweeteners like erythritol firm up as they cool, so give them at least 15 minutes before eating.