Preheat the oven to 180°C (350°F). Line a 12-cup muffin tin with paper liners or grease the cups.
In a large bowl whisk together flour, baking powder, baking soda, cinnamon, nutmeg, and salt until evenly combined.
In a separate bowl beat the eggs lightly, then whisk in sugar, oil, yogurt (or buttermilk), and vanilla until smooth.
Pour the wet ingredients into the dry ingredients and stir gently with a spatula until just combined; do not overmix.
Fold in the grated carrots and, if using, chopped nuts and raisins or pineapple until evenly distributed.
Spoon the batter into the prepared muffin cups, filling each about two-thirds full for a nice rise.
Smooth the tops lightly and, if desired, sprinkle a few extra carrot shreds or chopped nuts on each muffin.
Bake in the preheated oven for 18–22 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs.
Remove the muffins from the oven and let them cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.
Serve warm or at room temperature. Optionally top with cream cheese frosting once fully cooled.