Begin by preheating the oven to 375° F (190° C). Proceed to thoroughly spray a 24-cup mini muffin tin with cooking spray and set aside for later use.

In the bowl of a stand mixer, or using a handheld mixer, thoroughly beat the melted butter, both sugars, and Greek yogurt until the mixture achieves a smooth and homogenous consistency, approximately 2-3 minutes. Following this, incorporate the egg and vanilla extract, continuing to beat at a medium-high speed for an additional 2 minutes.

In a separate large bowl, whisk together the flours, cinnamon, salt, cream of tartar, and baking soda, ensuring a uniform mixture. Gradually, on a low speed, incorporate the dry ingredients into the wet mixture until fully combined, taking care to avoid overmixing.

Utilize a cookie scoop or measuring spoon to place precisely 2 teaspoons of the dough into each prepared mini muffin cup. Bake in the preheated oven for a duration of 10-12 minutes. Upon removing from the oven, immediately use the back of a tablespoon or teaspoon to press down on the top of each cookie cup, creating a round indentation.

Allow the cookie cups to cool within the pan for 5 minutes. Subsequently, remove them and transfer to a wire rack to cool completely.

In the bowl of a stand mixer, or using a handheld mixer, combine all ingredients for the cinnamon cream cheese frosting, excluding the powdered sugar. Beat together until smooth. Gradually add in the powdered sugar, continuing to beat until the mixture becomes smooth and achieves a fluffy consistency, roughly 4 minutes.

Once the cookie cups have cooled, either pipe or spoon the cream cheese frosting into them. If desired, garnish with sprinkles. For storage, place the finished cookie cups in an airtight container and refrigerate.