Preheat oven to 400°F. Coat 12 muffin cups with cooking spray.Whisk whole-wheat flour, all-purpose flour, baking powder, baking soda and salt in a large bowl.
Whisk eggs and brown sugar in a medium bowl until smooth. Add almond milk, orange juice, oil and almond extract. Whisk to blend. Add to the dry ingredients and mix with a rubber spatula just until moistened.
Scoop the batter into the prepared pan. Sprinkle with almonds.
Bake the muffins until the tops are golden brown and spring back when touched lightly, 15 minutes or until toothpick comes out clean when inserted into the center of a muffin
Loosen edges and turn muffins out onto a wire rack to cool slightly before serving.
Notes
I found this batter to be very, very loose - just make sure to not over mix. If you see a lot of lumps, it is ok...don't worry, they do disappear!