Preheat the oven to 375˚F. Line a muffin tin with paper liners or grease with non-stick cooking spray. Set aside.
Prepare the muffin batter. In a mixing bowl, combine the flour, cinnamon, cardamom, ginger, allspice, nutmeg, cloves, baking soda, and salt. Set aside.
In another bowl, whisk together the light brown sugar, Greek yogurt, applesauce, vegetable oil, eggs, and vanilla extract until combined.
Add the dry ingredients to the wet mixture. Stir using a rubber spatula until just combined and smooth. Don’t overmix the batter. Set aside.
Prepare the cheesecake filling. Add the softened cream cheese, powdered sugar, and vanilla extract to a mixing bowl. Whisk using a hand whisk or a fork until just combined. Transfer this mixture to a piping bag.
Divide the chai muffin batter between prepared paper liners or greased muffin tin until about 2/3 - 3/4 full. Then, fill each muffin with 1 tbsp of cheesecake filling. Swirl the filling with the batter on top of the muffin using a toothpick.
Bake in the preheated oven for about 15 minutes or until a toothpick inserted into the center comes out clean. Remove from the oven and let cool in the muffin tin for 10 minutes. Then, transfer to a cooling rack to finish cooling and prevent soggy bottoms. Enjoy!