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 buttermilk, orange juice, oil and vanilla; whisk to blend. Add to the dry ingredients and mix with a rubber spatula just until moistened.
Scoop half the batter into the prepared pan. Mix jam and almond extract; drop a generous teaspoonful into the center of each muffin. Spoon on the remaining batter, filling each muffin cup completely. Sprinkle with almonds, then sugar.
Bake the muffins until the tops are golden brown and spring back when touched lightly, 15 to 25 minutes. Loosen edges and turn muffins out onto a wire rack to cool slightly before serving.