Core and thinly slice one apple. Grate the other apple on the largest holes of a box grater. Make the batter following the instructions for the base recipe, stirring the poppy seeds, nutmeg, and cinnamon into the dry mixture and adding the grated apple to the wet mixture. Continue as directed, then scoop the batter into the muffin cups, arrange the apple slices over the top of the muffins, and sprinkle with poppy seeds. Bake as directed.
Buy nutmeg whole and grate it as needed. You’ll find that the flavor is much less harsh when nutmeg is freshly grated. Although you can purchase a special grater for nutmeg, you can simply use a Microplane zester.