Preheat the oven to 350F. Generously grease a muffin tray.
In a large bowl, whisk together the whole wheat flour, almond flour, baking powder, cinnamon, nutmeg, and salt.
In a medium bowl, combine the egg, yogurt, almond milk, coconut sugar, oil, and vanilla, whisking to combine. Pour the wet ingredients into the dry and mix until just combined.
Make the streusel topping:
In a medium bowl, combine the whole wheat flour, almond flour, coconut sugar, coconut oil, and cinnamon, mixing with a fork.
Divide the batter into the muffin tin, filling halfway, and sprinkling the streusel into the batter before adding more batter. Top with the remaining streusel.
Bake for 18 to 22 minutes, or until a toothpick comes out clean.