In a medium bowl, whisk together the flour, baking soda, baking powder, and salt. Set aside.
In a separate bowl, create a lemon sugar mixture by rubbing the sugar and lemon zest together between your fingers. Set aside ¼ cup of this lemon sugar for the cream cheese mixture. The remaining ¾ cup will go into the batter.
Mix the softened cream cheese, ¼ cup of lemon sugar, and 1 tablespoon of lemon juice in a medium bowl until smooth. Set aside.
In a large bowl, whisk together the eggs, vegetable oil, kefir, ¼ cup of lemon juice, vanilla extract, and the remaining ¾ cup of lemon sugar.
Gently fold the dry ingredients from step 1 into the wet ingredients just until the flour streaks disappear.
Add about ⅔ of the cream cheese mixture into the muffin batter and stir a few times to swirl it in.
Fill the muffin liners with batter so they're about ¾ full. Swirl the remaining cream cheese mixture on top of the batter (about 1 teaspoon per muffin).
Bake on the middle rack at 425°F for 5 minutes. Then, without opening the oven door, reduce the temperature to 350°F. Continue baking until a toothpick comes out clean (about 8-12 more minutes; 13-17 minutes total).
Once they're cool enough to touch, transfer them to a cooling rack.
Notes
Storage: Store fully cooled muffins at room temperature for up to 5 days or in the freezer for 1 month.Mini Muffins: Bake at 350°F for about 15 minutes.Jumbo Muffins: Fill jumbo muffin liners ¾ full and follow the same baking instructions as written. They make slightly take longer to bake.Lifeway Kefir: This recipe is sponsored by Lifeway Foods. I genuinely love their products and mission! If you can't find their kefir, you can substitute an equal amount of buttermilk.