I always start by preheating my oven to 375°F, since a hot oven is what gives these muffins that tall, domed top. While it heats, I line my muffin tin with paper liners so nothing sticks later. This little bit of prep saves me a headache when it's time to pull the muffins out.
In a medium bowl, I whisk together the flour, baking soda, salt, cinnamon, nutmeg, cloves, and ginger. Whisking the spices into the flour first means they get evenly distributed, so you won't bite into a clump of cinnamon in one spot. I set this bowl aside while I work on the wet ingredients.
In my large bowl, I whisk the pumpkin puree, sugar, oil, eggs, and vanilla until the mixture looks smooth and glossy. Then I pour the dry ingredients into the wet ones and fold everything together with a spatula, just until no streaks of flour remain. I try not to overmix here, since that's what keeps the muffins tender instead of tough.
While the batter rests, I beat the softened cream cheese, powdered sugar, and egg yolk together until it's completely smooth. I like to do this in a small bowl with a hand mixer, since lumps in the filling are the one thing that can ruin the texture. This filling is what makes these muffins feel special, so I don't rush this step.
I use my cookie scoop to add a layer of pumpkin batter to each muffin cup, filling them about halfway. Then I drop a spoonful of the cream cheese filling right in the center of each one. Finally, I top it off with a bit more pumpkin batter, just enough to cover the filling so it bakes in the middle instead of on top.
I bake the muffins for 20 to 22 minutes, until the tops are golden and a toothpick inserted into the pumpkin part (not the cream cheese center) comes out clean. My oven runs a little hot, so I start checking around the 18-minute mark just to be safe.
Once they're out of the oven, I let the muffins sit in the pan for about 5 minutes before transferring them to a wire rack. This short rest keeps them from falling apart, and it also lets the cream cheese center set up just a little more before you take that first bite.