Heat the oven to 175C / 350F. Line a 12-cup muffin tin with paper liners or grease well.
In a large bowl, whisk the flour, flaxseed meal, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt.
In a second bowl, whisk the eggs, applesauce, milk, melted butter, honey, and vanilla until smooth.
Pour the wet mixture into the dry and fold with a spatula just until combined. A few streaks of flour are fine, don't overmix or the muffins turn gummy.
Fold in the diced apple until evenly distributed through the batter.
Divide the batter among the 12 muffin cups, filling each about two-thirds full.
Bake for 20 to 22 minutes, until the tops spring back and a toothpick inserted in the center comes out clean or with a few moist crumbs.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely before storing.