With the rack in the middle position, preheat the oven to 350°F (180°C). Line 18 muffin cups with paper or silicone liners.
In a bowl, combine the flour, baking powder, baking soda and spices.
In a large bowl, whisk together the eggs, brown sugar, milk, oil and molasses. Add the cereal and let soak for 5 minutes. Add the dry ingredients all at once and stir with a spatula, just enough to moisten the flour. Stir in the apples.
Using a 1/3-cup (75 ml) ice cream scoop, spoon the batter into the muffin cups. Bake for 25 minutes or until a toothpick inserted in the centre of a muffin comes out clean. Let cool on a wire rack.
Recipes with the "Healthy Pick" stamp have been evaluated by a registered dietitian member of the Ordre professionnel des diététistes du Québec.