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Layered Cream Cheese Cupcakes

Layered Cream Cheese Cupcakes

Who doesn’t love cupcakes? I’m not a huge fan of overly sweet frostings, however. In fact, I’m not really a sweets person, so whenever I do indulge in a dessert I prefer it to not be too sweet. It’s easy to add on sweetness, but it’s tough to take it away.

These are a sweet treat for breakfast or whenever you want a snack. They also freeze well for those times when unexpected guests come over and you have nothing prepared for dessert.

It’s also a great idea for parties, especially for younger kids. I like to put fun decorations on top of cupcakes, rather than putting gobs of frosting on top of the cupcake. This is also a good idea for portion control. Too often I find myself unaware that I’ve eaten more food than I intended. Having these little cupcakes around is a lifesaver. Of course, I usually have to hide the rest or I’ll end up eating them all, in spite of my good intentions.

These are a crowd pleaser for kids and adults. Once the kids get over the lack of frosting, they end up loving the crunch of the topping. Not surprising, adults can’t help but take a few home with them.

Cupcake Batter:

  • 1 cup of unsalted butter (if you use salted butter, don’t add any extra salt)
  • 2/3 cup white sugar
  • 2 large eggs
  • ¼ cup yogurt
  • 1 cup all purpose flour
  • 1 cup whole wheat flour
  • 2 teaspoons baking powder
  • ¼ teaspoon salt
  • ½ teaspoon cinnamon


  • 16 ounces cream cheese, softened
  • 1 large egg
  • 2/3 cup white sugar
  • 1 teaspoon vanilla


  • ½ cup sugar
  • 1 cup flour
  • ½ teaspoon cinnamon
  • ½ cup butter, softened


  1. Preheat the oven to 350F. Make sure the rack is in the middle.
  2. Place muffin papers into pans.
  3. Cream butter and sugar together until fluffy, about 3-4 minutes. Make sure to scrape it down once in a while. Add eggs one at a time, mixing well before adding another. Add yogurt.
  4. Combine the flours, baking powder, salt, and cinnamon in a bowl. Use a whisk to mix it up together and to break up any lumps.
  5. Add the flour mixture to the creamed mixture, a bit at a time; beat it well—the batter will be pretty thick.
  6. Scoop a small amount of batter into the bottom of each muffin cup. I use a cookie scoop for this.
  7. In another bowl make the filling: cream together the cream cheese, egg, sugar, and vanilla.  Make sure it’s well combined and fluffy. Gently spread on top of the first batter layer.
  8. Dot the remaining batter on top of the filling layer.
  9. Mix all the topping ingredients: sugar, flour, cinnamon, and butter,  and sprinkle them evenly over the cupcakes.
  10. Bake the cupcakes for about 20 minutes or until the middle is set. You can use a toothpick to test for doneness as well.
  11. Let cool on a rack for a few minutes before removing from the pan to cool completely.