Position oven rack in the middle of the oven.Preheat oven to 400 degrees.Line 12 cup muffin tins with paper liners.In a large bowl,whisk flours,baking powder,salt,and flaxseed to combine.Add berries and stir to coat.
In another bowl,whisk flours,baking powder,salt,and flaxseed to combine.Add berries and stir to coat.In another bowl,whisk eggs,milk,sugar,oil,and vanilla extract to combine.
Pour egg mixture into berry mixture and gently mix with a fork to moisten dry ingredients.Don't overmix, a few lumps in the batter are normal.Spoon into muffin cups.
Bake until muffins are puffed and wooden toothpick inserted into center comes out clean, 20 to 24 minutes.Cool 5 minutes on rack before serving. Makes 12.