Heat oven to 375/ Line a 12-cup muffin pan with cupcake liners and lightly coat with cooking spray.
Pulse 1 cup oats in food processor until very fine; place in a large bowl. Whisk in flax meal, nutmeg, cinnamon, salt and baking powder. Stir in half of the pecans.
In a medium bowl, whisk together oil, and honey. Whisk I eggs vanilla nd milk. Add wet ingredients to dry ones and mix to combine, then fold in apples and remaining 1 cup oats.
Divide batter among liners (about a heaping 1⁄4 cup each) and top with remaining pecans. Bake until tops no longer look shiny, 20 to 25 minutes