Preheat the oven to 350˚F. Line a baking sheet with parchment paper and set aside.
In a medium bowl, mix together the flour, baking soda, cinnamon, ginger and cloves.
In the bowl of a stand mixer, cream together the sugar, peanut butter and butter until light and fluffy. Mix in the egg, egg yolk, molasses and vanilla.
Slowly mix in the dry ingredients until fully incorporated.
Using a cookie scoop, scoop the cookie dough onto the prepared baking sheet. Bake in the preheated oven for 10-12 minutes, or until the edges are firm. Allow to cool on the baking sheet for around 5 minutes, then transfer to wire racs to cool completely.