Preheat oven to 400 degrees Fahrenheit. 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 milk with vinegar, orange juice, oil, and vanilla; whisk to blend. Add to the dry ingredients and mix with a rubber spatula until just moistened.

Scoop half the batter into the prepared muffin pan. Mix jam with vanilla; drop a generous teaspoonful in the center of each muffin. Spoon the remaining batter over the jam, covering it completely and filling the wells about three-quarters full. Sprinkle with almonds, then sugar.

Bake muffins until the tops are just golden brown, 17 to 20 minutes.