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 cream cheese 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!
One reader, Amanda, commented: “Wow, this is amazing! So moist with just the right touch of spice and cheesecake hiding inside… My garden zucchinis have never been put to better use. ★★★★★“
One reader, Dee, commented: “These muffins turned out amazing!! The extra crunch from the coarse sugar on top, paired with the cinnamon flavor of the fluffy muffin and creamy texture from the cream cheese all worked so well together. Will definitely be making these again! ★★★★★“
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 brick 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 12-count 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, zucchini cake, or peanut butter chocolate chip zucchini bread next! For something savory, you’ll love these zucchini fritters, this feta & herb zucchini casserole, or these zucchini biscuits. For even more inspiration, here are 20+ sweet and savory zucchini recipes to browse.
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.
Cream Cheese Zucchini Muffins
- Prep Time: 15 minutes
- Cook Time: 22 minutes
- Total Time: 55 minutes
- Yield: 10 muffins
- 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
- 1 and 1/2 cups (188g) all-purpose flour (spooned & 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 (150g) shredded zucchini (no need to blot)
- optional: coarse sugar for topping
Cheesecake Filling
- 5 ounces (142g) full-fat brick cream cheese, softened to room temperature
- 1 egg yolk, at room temperature
- 1/2 teaspoon pure vanilla extract
- 3 Tablespoons (36g) granulated sugar
Instructions
- 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.
Notes
- 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.
- Special Tools (affiliate links): 12-count Muffin Pan | Muffin Liners | Glass Mixing Bowls | Whisk | Electric Mixer (Handheld or Stand)
- 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.
Reader Comments and Reviews
Currently eating my second one straight out of the oven. These are to die for. And also toddler approved! Absolutely making these again.
Hi Sally,
I have a lot of left over spreadable cream cheese, can I use it in place of block or will it ruin the recipe? Thanks!
Hi Debbie! Spreadable cream cheese has a much higher water content and isn’t right for this recipe. Best to stick with block cream cheese!
Great, thank you!
Delicious! Love the cream cheese filling!
These are great! I shared some and got really nice compliments! Thank you for specifying the weight of shredded zucchini. Most recipes don’t and I never know how tightly it should be packed into the measuring cup.
This recipe is for sharing with friends and keeping! Very flavorful, fun to have frosting in the middle, and it’s worked with freshly shredded zucchini and zucchini shredded a day ago and refrigerated overnight (yup, already made it twice). It made twelve muffins for us each time.
Definitely follow the instruction for high heat for the first few minutes, and probably err on the side of an extra minute or two if you’re not sure about your oven. My muffins puffed up nicely, but fell a bit after baking was complete.
These are going to be made until the end of zucchini season in Napa!
I had never made a filled muffin before, but Sally gives great instructions, and I have developed a lot more confidence under her tutelage! The muffins are delicious. Thanks again, Sally!
If you make this into a loaf instead of the muffins do you still bake at 425 or 350 like the loaf recipe suggests?
Hi Tracy, for a loaf, follow the bake time and temperature for Zucchini Bread (350 degrees for 45-55 minutes). Enjoy!
Super Moist! Delicious! My batter seemed dry so I added less than 1/4 cup of buttermilk. I also had to substitute cottage cheese in place of cream cheese because I didn’t want to make a grocery store run just for that.
I have made this 3 times the 1st. Time it was delicious 2nd time it was very dry. 3rd. Time it didn’t have enough to cover the top. Please tell me what I am doing wrong.
Hi Glenda, are you changing any of the ingredients from batch to batch? If the muffins are coming out dry, be sure to 1) spoon and level your flour and 2) not to over bake. Both can contribute to overly dry baked goods.
These were delicious! I used frozen grated zucchini, thawed and then drained, and they turned out great. I also ran out of canola oil and had to use some EVOO, but it did not affect the flavor.
This recipe calls for vegetable oil. Can I use butter or Ghee instead? Thanks!
Same amount of melted butter works!
These muffins turned out amazing!! The extra crunch from the coarse sugar on top, paired with the cinnamon flavor of the fluffy muffin, and creamy texture from the cream cheese all worked so well together. Will definitely be making these again!
These muffins are the best I have ever made. Really moist and flavourful without being too sweet.
Wow these are AMAZING.
The only nitpick I have is that the batter was super dry and thick so I had to add probably 1/4 cup milk. I had the same issue with the regular zucchini bread recipe from your site. I wonder if it’s because I’m using melted coconut oil instead of canola?
This zucchini recipe is hands down the best muffin recipe I have tried. The additional layer of cream cheese caught my attention. While adding the cream cheese deviated from my quest for healthy the rave reviews won me over. The only change I made is that I did use 1/4 cup oil and 1/4 cup unsweetened applesauce. Otherwise following everything else in the recipe and Sally’s baking directions, the result were some amazing muffins. It is in my keeper file.
Hi Sally! I tried making this as a loaf using your zucchini bread recipe as you suggested. How do I prevent the top layer of my cake from sinking into my middle cream cheese layer? Should I pour less zucchini batter on the bottom and save more for the top?
Hi Jasmine! Adding more zucchini batter on top of the cream cheese layer would certainly help. And/or you can try adding 2 Tablespoons of flour to the half of the batter you are using for the top layer. A thicker, stronger batter on top would help prevent it from sinking too much. (Likewise, make sure you bake the bread long enough. Under-baked breads will sink a they cool.)
Can I use the full 8 ounce block of cream cheese rather than splitting it and only using 5 ounces? Would I need to add more egg yolks in this case?
Yes, you’d have to add more of the other filling ingredients as well. But then you will have too much cream cheese filling for the amount of zucchini batter. Try doubling the zucchini batter or even 1.5x the recipe to have enough.
Do these needed to be refrigerated, with the cream cheese filling, or do you not need to since it’s cooked?
Hi Lynn, You can cover leftover muffins tightly and store at room temperature for up to 2 days, or if you need to store them longer you can keep them in the refrigerator for up to 1 week.
Absolutely delicious, and very easy to whip up!
I love all your recipes but I made these and after 5 minutes out of the oven they collapsed and had big holes in them. Did I do something wrong.
Just, wow! I took it one more step and made a meringue with the leftover egg white. I layered a spoonful of the meringue on top of the cream cheese mixture, then topped it with the batter.
Hi Sally I made these muffins with carrot instead of zucchini and they were amazing!! I have never enjoyed baking so much since I found your site through one of the you tubers I subscribe to.
These are so delicious! My 2 and 7 year old love them as well. I made a double batch the second time I made them because one dozen didn’t last long the first time! Another wonderful keeper recipe, Sally!
Just made this recipe…DELICIOUS!
They taste so good, the quantity of spices is on point!!
With the cream cheese filling it’s PERFECT!
Thank you Sally, can’t wait to try another recipe next week 🙂
Excited to see how these turn out I added about 1/4 c chocolate chips to the cream cheese.
I made these muffins today. They came out delicious! I added some walnuts into the batter, which turned out to be a good addition. This is a great recipe. I will definitely be doing these again.
I’ve tried almost all your muffin recipes and can’t decide which one I like best, but this one is delicious (the best banana bread muffin version and the pistachio cupcakes turned into muffins with your oven trick are incredible too!) ! I’ve done this recipe twice with cream cheese and mascarpone and I go for the mascarpone one but both are hilarious! Thanks so much Sally!!! Greetings from Barcelona!
Absolutely delicious!
The best muffins ever! Thank you so much for the great recipe!!!
Made these for my husband (first time ever cooking or baking with zucchini) and he LOVED them! I saw your similar pumpkin cheesecake muffin listed in the article, but can I just switch the zucchini from this recipe with pumpkin?
Hi Jane! That shouldn’t be a problem, but I would reduce the pumpkin puree down to 3/4 cup.
I can’t wait to make this! Can I reduce the amount of sugar so I feel better about giving it to my kids? By how much?
Hi Nancy, You can try reducing the sugar but keep in mind that the texture will change and the muffins won’t be as soft. You may want to look at this Greek Yogurt Zucchini Bread which uses agave instead of granulated or brown sugar – see the recipe notes to make it as muffins.
I decided to go ahead and make these and they were AMAZING! I actually made 12 large muffins rather than 10 out of the batter.
This recipe is absolutely delicious. It reminds me of a muffin with cream cheese filling I used to get at a local coffee shop that has since closed. I am so excited to try this with ingredients other than zucchini when zucchini goes out of season.
I just made this and although they were awesome it looked like the batter was too thick idk I put more oil in and it was a small batter only made eight cupcakes not too small