In a large mixing bowl, whisk together the pumpkin purée, eggs, brown sugar, granulated sugar, oil, milk, and vanilla extract. Mix until smooth and well combined. This mixture should look creamy and golden orange.
In a separate bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, and cloves. Make sure the spices are well distributed for even flavor throughout the muffins.
Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined—don’t overmix. Fold in the diced apples and any optional add-ins like nuts or chocolate chips. The batter will be thick and textured.
Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners or lightly grease it. Spoon the batter evenly into the cups, filling each about 3/4 full.
Bake for 20–22 minutes, or until a toothpick inserted in the center comes out clean. Let them cool for 5 minutes in the pan before transferring to a wire rack.