Using my go-to zucchini bread recipe as the starting point, these soft cream cheese zucchini muffins are deliciously spiced with cinnamon and stuffed with a cheesecake style filling. Before baking, sprinkle with coarse sugar for a little sparkling crunch on top.
Zucchini Muffins, Upgraded
These muffins are downright DELICIOUS. Using a variation of my absolute favorite zucchini bread recipe—an old family recipe that won 1st place in a state fair—we’re baking muffins stuffed with sweet cream cheese. They taste like dessert! I got the recipe idea from these pumpkin cheesecake muffins, a total fall favorite. Here we’re swapping pumpkin for zucchini and skipping the crumb topping. Though you could definitely add it here if desired!
Here’s why you’ll love them:
- Easy muffin batter using basic ingredients
- Soft, moist, filled with creamy filling
- Warm spice flavors like cinnamon and nutmeg
- Recipe makes just 10, but can easily be doubled
- Hidden veggies—you can’t taste the zucchini!
Overview: How to Make Cream Cheese Zucchini Muffins
Today’s muffin recipe is similar to my regular zucchini muffins. The batter yields slightly fewer muffins, but if you want a full dozen, you can use the plain zucchini muffins batter and stretch the cream cheese filling to fill all 12.
The full written recipe is below, but let’s quickly walk through the steps first.
- Make the zucchini batter: All basic ingredients here including flour, leaveners, egg, sugar, and vanilla. Compared to my zucchini bread batter, I add a little more baking powder so the muffins can rise up under the heavy cream cheese filling. I use a mix of brown sugar and granulated sugar for extra flavor—and I actually slightly reduced the amount of sugar since we’re adding the sweet cream cheese filling. Cinnamon and nutmeg add flavor. Use a box grater to shred the zucchini. I add a little extra zucchini for added volume.
- Make the cream cheese filling: You need 4 simple ingredients for the cream cheese filling. Bring 5 ounces of block cream cheese to room temperature, then beat it with 1 egg yolk, sugar, and a touch of vanilla extract. The egg yolk helps the cream cheese filling “set” like cheesecake. Don’t use a whole egg—the texture will taste off.
- Assemble: Layer a heaping Tablespoon of zucchini batter into your lined muffin pan. Top with a Tablespoon of filling, then another heaping Tablespoon of zucchini batter. No need to swirl together. I always sprinkle crunchy coarse sugar on top because it adds a lovely contrast on the super soft muffins. I like Sugar in the Raw or white sparkling sugar sprinkles, which you can usually find with the sprinkles in the baking aisle.
- Bake: Your kitchen will smell divine!
Layer the zucchini batter and cream cheese batter together in your muffin liners. This recipe yields 10 muffins.
Try my zucchini crumb cake next!
- Carrot, Apple, or Banana: You can replace the shredded zucchini with shredded carrot for cream cheese carrot muffins. I always like a little ginger with carrot, so feel free to add 1/4 teaspoon of ground ginger to the carrot batter. You could replace the zucchini with shredded apple, too! This cream cheese filling would be wonderful with my banana muffins batter as well. For banana, carrot, or apple, follow the baking instructions and time(s) written below.
- Loaf instead of muffins: Use my zucchini bread recipe and feel free to skip the chocolate chips. Add half of the batter to the greased 9×5 inch loaf pan, spoon and gently spread this cream cheese filling on top, then carefully spread remaining zucchini batter on top. Use a toothpick or knife to swirl together, which will prevent the loaf from separating. (Not necessary for muffins.) Add about 5 minutes to the bread’s bake time.
- Double the recipe: To yield about 20-22 muffins, feel free to double the recipe below by doubling each ingredient. Instead of 2 egg yolks in the cream cheese filling, 1 full egg will work.
Layer zucchini batter and cream cheese filling together to make cream cheese zucchini muffins. These super soft and moist muffins are deliciously spiced with cinnamon and taste wonderful with a crunchy coarse sugar topping.
- 1 and 1/2 cups (188g) all-purpose flour (spoon & leveled)
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
- 2 teaspoons ground cinnamon
- 1/4 teaspoon ground nutmeg
- 1/2 cup (120ml) canola or vegetable oil
- 1/4 cup (50g) packed light or dark brown sugar
- 1/2 cup (100g) granulated sugar
- 1 large egg, at room temperature
- 1 teaspoon pure vanilla extract
- 1 and 1/4 cups (about 175g) shredded zucchini (1 medium zucchini, no need to blot dry)
- optional: coarse sugar for topping
- 5 ounces (140g) block cream cheese, softened to room temperature
- 1 egg yolk, at room temperature
- 1/2 teaspoon pure vanilla extract
- 3 Tablespoons (36g) granulated sugar
- Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. This recipe yields about 10 muffins.
- Make the zucchini batter: Whisk the flour, baking powder, baking soda, salt, cinnamon and nutmeg together in a large bowl. Set aside. In a medium bowl, whisk the oil, brown sugar, granulated sugar, egg, and vanilla extract together. Whisk in the zucchini. Pour the wet ingredients into the dry ingredients and whisk or stir until just combined. Avoid over-mixing.
- Make the cream cheese filling: Using a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese in a medium bowl on medium-high speed until smooth and creamy. Beat in the egg yolk, vanilla extract, and sugar until combined.
- Spoon 1 heaping Tablespoon of zucchini muffin batter into the muffin cups. Layer with 1 Tablespoon of cream cheese filling, then another heaping Tablespoon of muffin batter—or however much batter is needed to fill the cups all the way to the top. Some cream cheese filling can poke out of the top or on the sides. Sprinkle with coarse sugar, if desired.
- Bake for 5 minutes 425°F (218°C) then, keeping the muffins in the oven, reduce heat to 350°F (177°C)* and continue baking for another 15–17 minutes. The total time these muffins should be in the oven is around 20-22 minutes. Allow to cool for at least 10 minutes in the pan before serving.
- Cover leftover muffins tightly and store at room temperature for up to 2 days, or in the refrigerator for up to 1 week.
- Freezing Instructions: For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator, then heat up in the microwave if desired.
- Zucchini: I do not peel the zucchini before shredding, but you certainly can if you’d like.
- Variations or Doubling the Recipe: For other flavor ideas, turning this into a loaf, or doubling the recipe, see Possible Variations above.
- Why the initial high oven temperature? Like I do for most muffin recipes, bake the muffins for 5 minutes at a very hot temperature. Then, keeping the muffins in the oven, switch to a lower temperature for the remaining bake time. This initial high temperature will quickly lift the muffin tops so they’re extra high, then the centers will bake during the lower temperature bake time. This trick makes beautiful bakery-style muffins every time.
Keywords: cream cheese zucchini muffins