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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.

stack of cream cheese zucchini muffins

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!
cream cheese zucchini muffins

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.

  1. 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.
  2. 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.
  3. 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.
  4. Bake: Your kitchen will smell divine!
shredded zucchini with box grater
cream cheese and zucchini muffin batter

Layer the zucchini batter and cream cheese batter together in your muffin liners. This recipe yields 10 muffins.

cream cheese zucchini muffins batter
zucchini muffins stuffed with cheesecake filling

Try my zucchini crumb cake next!

Possible Variations

  • 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.
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cream cheese zucchini muffins

Cream Cheese Zucchini Muffins

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 22 minutes
  • Total Time: 55 minutes
  • Yield: 10 muffins 1x
  • Category: Dessert
  • Method: Baking
  • Cuisine: American

Description

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.


Ingredients

Scale
  • 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

Cheesecake Filling

  • 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

Instructions

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. Cover leftover muffins tightly and store at room temperature for up to 2 days, or in the refrigerator for up to 1 week.

Notes

  1. 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.
  2. Zucchini: I do not peel the zucchini before shredding, but you certainly can if you’d like.
  3. Variations or Doubling the Recipe: For other flavor ideas, turning this into a loaf, or doubling the recipe, see Possible Variations above.
  4. 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

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Reader Questions and Reviews

  1. Sally, you deserve a 10 star rating for these delicious muffins! You make deciding on a favorite muffin
    Next to impossible!!! These are sp soft, I feel like I am eating cheese cake muffins!
    My friends and family love to see me coming when I have goodies. I need physical therapy often and I bring treats to all the therapists, I am their “goodie fairy”
    Thanks to your recipes with all the tips and your posts with such informative information about baking I have progressed from being a good baker to a great baker!
    I named my kitchen “Busy Bee Bakery”

    1. So happy to read this, Nancy! And it’s so wonderful that you’ve expanded your knowledge of and experience with baking using my recipes. Thank you very much!

    2. These were awesome!! However, I have a question. My cream cheese always looks curdled when I beat it. Any idea what I’m doing wrong? I do bring it to room temp as well.

      1. Hi Holly! We’re happy to help troubleshoot. Make sure you are using high quality, full fat cream cheese. Sometimes it may take longer to beat until it’s smooth, so don’t be alarmed if it takes a bit longer to beat. Hope this helps and we’re so glad you enjoy these muffins!

      2. I made these last night and added some fresh picked blueberries. They are so very delicious!!
        All the stars! Will absolutely make time and time again!

  2. Li vorrei provare ma non so in Italia quale formaggio posso usare?

    I’d like to try them but I don’t know which cheese I could use in ItalY

    1. Hi Patrizia, In the U.S. block cream cheese is very different than the tubs and is the only cream cheese that will work in most of our recipes. We have been told by readers outside the U.S. that cream cheese in a tub is different from ours and can work, but we have not tested it. If you have that available, we would recommend giving that a try. Please let us know if you do!

  3. These muffins are the BEST!!! I didn’t have AP flour, so I substituted whole wheat flour; it turned out great! Thank you for this amazing recipe, it’s going to be my family’s staple (esp. during the summer when we have zucchini coming out of our ears).

  4. I love this recipe they taste so good but everytime I make them they sink in the middle after they cool. Am I doing something wrong?

    1. Hi Christine! The cream cheese filling certainly weighs down the muffin and a couple muffins— in any batch we make— tend to sink a bit. A little longer in the oven helps or even a bit less cream cheese filling in each muffin.

    1. Hi Tara, feel free to double the recipe by doubling each ingredient. Instead of 2 egg yolks in the cream cheese filling, 1 full egg will work.

      1. Thank you. I couldn’t wait so went ahead and doubled everything. Just took them out of the oven and they look fantastic. Cheers.

      2. Hello, what would the amount of batter/ filling to make jumbo muffins? Baking time? Wanting to make for bake sale

  5. I swapped out the cream cheese stuffing and instead used lemon curd. Fantastic! The zucchini part is light and tasty, and the lemon flavor complimented it nicely. Will make them again. Thank you!

  6. i just baked them,, I replaced the zucchini for carrot and apple and i didn’t have agave so i used 120g of brown sugar, they came out great but the batter wasn’t that consistency as yours, i wonder if i should use extra oil next time. because i like using brown sugar. any recommendation?? thank a lot!! your recipes are amazing..

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