Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with parchment paper liners.
In a medium-sized bowl, sift together the whole wheat pastry flour, baking powder, and salt.
In a separate large mixing bowl, whisk together the Greek yogurt, maple syrup, egg, and vanilla extract until the mixture is homogeneous.
Gradually incorporate the dry ingredients into the wet mixture, alternating with additions of the almond milk, stirring until just combined.
Divide the batter evenly among the 12 prepared cupcake liners, filling each approximately two-thirds of the way.
Bake for 18 to 20 minutes, or until the tops spring back when lightly touched and a toothpick inserted in the center comes out clean.
Remove from the oven and allow cupcakes to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.