Cream Cheese Zucchini Muffins

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

I’ve been holding onto this recipe since last summer and I’m thrilled to finally have it photographed and ready for you to try it!

Zucchini Muffins, Upgraded

These muffins are downright DELICIOUS. Using my absolute favorite zucchini bread (and muffins) 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 a fall favorite: these pumpkin cheesecake muffins. 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

If you’ve made my zucchini bread recipe before, you know how easy this batter comes together. The 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 shredded 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 just 10 muffins. By the way, here are all of my recipes using zucchini.

Try my zucchini crumb cake next!

cream cheese zucchini muffins batter

zucchini muffins stuffed with cheesecake filling

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
  • Category: Dessert
  • Method: Baking
  • Cuisine: American


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

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


  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.


  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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  1. I feel like your blog should be called “Sally’s cream cheese addiction” lol. These sound really good though! Do you think it would work with your Greek yogurt zucchini batter? That ones my favourite! In fact, I’m planning on making a double batch for my freezer tomorrow. Best of luck with your new baby!

    1. Thanks Stephanie! The Greek yogurt zucchini bread batter should work just fine with this filling.

  2. This recipe looks delicious. I noticed that you can turn it into a loaf. Can you also make a loaf with the batter for your giant raspberry chocolate chip muffins? I’ve been making muffins, but it is easier to store loafs in the freezer!

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Judy, Sure can! For the raspberry chocolate chip muffins you’ll have too much batter for 1 loaf, so I recommend 2 9×5 inch or 8×4 inch loaves. I’m unsure of the best bake time, but use a toothpick to check for doneness. Bake at 350°F (177°C) the whole time.

      1. Thank you so much. Next time that I make them, they’ll be loaves!
        Stay safe and well, Sally. Wishing you a very easy delivery and a wonderful summer.

  3. I really like zucchini and I use it very often in my kitchen. Most often I add it to some dishes like pastas or casseroles but this recipe seems incredible for me. I started using zucchini when my husband grew then for the first time in our yard..Then it became our small obsession but it’s not a problem as zucchini are very healthy! Usually we grow this variety: because it is very early..It’s perfect in our climate! I have freshly picked zucchini so tomorrow I am preparing this dish! See in the comments that it will be so tasty!

  4. I have never jumped on a recipe this fast but we just picked zucchini from our garden last night with plans to bake today, and this recipe arrived right in time. The steps were easy to follow (I made these exactly as the recipe says), and the muffins turned out moist and delicious. The cream cheese is the perfect addition. The bake time was accurate–they took 20 minutes and the tops puffed up perfectly. Thank you for another reliable recipe. I know we’ll make these again and again!

  5. Mildred Rogers says:

    I made these muffins with gluten free flour and they were delish!

  6. Made these today and they are delicious! My first time ever making or eating zucchini in a baked good. Hopefully soon I will make your chocolate zucchini cake, I have been eyeing it for a while now.

  7. Seriously the best muffins I’ve ever had!!!

  8. Ashley Thomas says:

    Just made these and they are so good! Instead of using all white flour, I used 1 cup of whole wheat pastry flour and 1/2 cup of all-purpose white flour. They still turned out great and super soft! I also omitted the sugar on top before putting in the oven, and they were still sweet enough without it. Great recipe!

  9. Just made these and they are ABSOLUTELY DELICIOUS. They were a hit in my house! I made them with fresh zucchini from my garden. Definitely a must-try. Sally, thank you once again! Your recipes are always so good!!

  10. Just made these yesterday. They are wonderful! Such a terrific texture and flavor. Great recipe Sally!

  11. These were SO GOOD and so easy to make. I made the recipe exactly as described.
    The mix of the cream cheese filling swirled in is HEAVENLY. If you love zucchini bread, you’ll love these muffins.

  12. Hi Sally. Could this be made in a jumbo muffin tin? If so, how many would it yield do you think? Any tips?

    1. Hi Hannah, I’d say about 5 jumbo muffins. I recommend following the baking times/temperatures for my jumbo blueberry muffins.

  13. . Saw your recipe and had to try it-love anything with cream cheese. The recipe produced muffins with excellent taste and texture (and maybe they are even healthy!). It made 12 muffins for me-just the right size for us. And the high temp for 5 minutes is a winner-never fails. Thanks again for another hit.

  14. Can I use the lower fat neufchatel cheese instead of regular cream cheese? Cannot wait to make these!

    1. Hi Ruthie! You can, but I find the cream cheese filling isn’t as smooth and creamy. Won’t make a huge difference though!

  15. DELICIOUS. I was skeptical at first how that amount of oil would ever combine with all those dry ingredients, but it did! Fun recipe to make, and my wife and toddler love them. The trick with baking at high heat for the first bit and then lowering is ingenious too. I’ve seen that in several other recipes here, but never outside Sally’s recipes. She’s got some skills that’s for sure.

  16. Sally, these muffins are absolutely delicious! They were a massive hit! Will most definitely make these again. Thank you for another great recipe

  17. Dianna Wissinger says:

    Hi Sally, I hope you are well. I made the cream cheese zucchini muffins today. They collapsed at the top/
    middle. Any ideas? All I could think of was I didn’t bake them long enough. I appreciate your help.

    1. Hi Dianna! Thank you so much for trying this recipe. The cream cheese filling certainly weighs down the muffin and a couple muffins— in any batch I make— tend to sink a bit. A little longer in the oven helps or even a bit less cream cheese filling in each muffin.

  18. We planted one zucchini that produces SO much we ran out of ideas… Glad I came across this recipe. So easy to make and DELICIOUS!

  19. Let me start by saying that I’m challenged with baking muffins. I don’t know what it is, but I just can’t get them right. I can bake other desserts but for whatever reason the humble muffin evades me. So hard to strike the right balance of light and moist, perfect crumb, and great flavour. These muffins delivered. Even my non-muffin eating kids devoured these.
    Thanks Sally for a great recipe. I will be saving for future garden bounty!

  20. I have leftover cream cheese frosting from your carrot cake recipe. Can I just thaw and use that instead?

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Janice, The cream cheese filling really needs the egg yolk. The egg yolk helps the cream cheese filling “set” like cheesecake.

  21. I made these over the weekend and they were great! I even forgot to lower the oven temp until the last 10 minutes and they still turned out perfectly! Thanks!

  22. Sally, this recipe is perfection. You are a great baker. Hats off. The trick for the nicely domed tops? Amazing. Even in my wonky oven these muffins came out beautifully. I added chocolate chips, because I can’t have muffins without them. Next time I will cut back on the spices, because that flavor profile is not my thing.

  23. Sarah Stengel says:

    Made GF by using bob’s 1:1 flour, added the extra egg white from the cream cheese mixture to the muffin mixture, added 1/2 c of applesauce. I also used 8oz cream cheese and just added an extra 1tbsp of sugar to that. Turned out wonderful. Thanks for a great recipe.

  24. Loved this muffin! They were delicious.

  25. Just made these. They are wonderful. Ran out of muffin liners, so two of them were just in the tin. Even with greasing generously, they didn’t make it out. They were still super tasty! Would definitely make again!

  26. Overall very tasty – I added some lemon zest And a few drops of juice to the cream cheese. The tops pulled away from the cream cheese Making a hollow space between the two layers. Any thoughts on why this occurred? Guess I will have to make another batch 🙂 the first one went quick!

  27. Do you happen to have nutritional information for this recipe? It was delicious!

    1. Hilari @ Sally's Baking Addiction says:

      I’m unsure of the nutritional info of this recipe, but there are many great online calculators like this one:

    2. Julie Taylor says:

      I dislike people that rate a recipe after listing All the modifications they’ve done to change it. The
      ese recipes on Sally’s site don’t require modification they are fantastic as they are but they can be tweaked to adjust your needs whether you add chocolate chips, nuts or cranberries those are just additives you don’t need to change these recipes at all.

  28. Wow this is amazing! So moist with just the right touch of spice and cheesecake hiding inside. Of course I had to use the streusel topping. My garden zucchinis have never been put to better use.

  29. This was my first time baking with zucchini – I was a little nervous because the batter was thick and a bit sticky but OMG THESE CAME OUT SO GOOD!!! One of the best muffin recipes I’ve made. Absolutely loved the cream cheese and spices. Sally, your recipes never disappoint!

  30. Julia Masse says:

    Absolute favorite zucchini recipe! I modified it by lowering the fat with yogurt, using Truvia baking blends for sugar replacement & then I added applesauce plus a bit of almond milk to make up for the lack of moisture since I used Truvia. Absolutely delicious & only 136 calories per muffin.

    1. Julia how much applesauce and almond milk did you use??

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I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally