Preheat oven to 375°F and line a 12 cup muffin tin with muffin papers.
In a large bowl, whisk together flour, sugar, baking powder, cinnamon, baking soda, salt, ginger, cloves and nutmeg. Then mix in 1/4 cup (50 mL) of the pumpkin seeds.
In separate bowl, whisk together the wet ingredients: eggs, pumpkin puree, oil, milk, and vanilla. Pour over dry ingredients and stir just until dry ingredients are moistened.
Spoon into prepared muffin cups. Sprinkle with remaining pumpkin seeds. Bake in center of a 375°F (190°C) oven about 20 to 25 minutes or until muffins are golden and tops are firm to the touch. Let cool in pan on rack for 5 minutes before transferring to a wire rack to cool.
While the muffins are baking, whisk together the cream cheese, confectioner’s sugar, vanilla, and lemon juice. (If the frosting is too thick, add a bit more lemon juice. If too runny, add more confectioner’s sugar.) Set aside.
When muffins are cooled completely, inject each muffin with a generous amount (1-2 tbsp) of cream cheese frosting and enjoy!