Zucchini Cream Cheese Muffins

5 from 1 vote

Do you still have zucchini in your garden? Or sitting on your counter? These muffins are the perfect way to use it up!

Zucchini Cream Cheese Muffins - a fast and easy breakfast recipe! Throw one in a lunchbox for back-to-school!


Oh my gosh. School starts in a week and a half! How did it become August so soon? Don’t get me wrong, I’m sooooo looking forward to school. It means a regular schedule for everyone and a lot less yelling from me.

School is going to save my vocal cords. #keepingitreal

Why do I yell? I get angry. Why? Because I swear no one listens to me.

I cannot wait for the peace and quiet and order that school brings. Even if it means that I have to make lunches again every evening. It’ll be worth it.

Can I get a heck yeah?


Zucchini Cream Cheese Muffins - a fast and easy breakfast recipe!

Speaking of lunches, and breakfasts for that matter, did you know that muffins are perfect for lunch boxes? It’s like getting a healthy cupcake for lunch. Getting a muffin in their lunch makes kids a rockstar in the cafeteria.

Pretty much that means you should make these muffins and send them to school with your kids. They’ll be a rockstar and come home excited and they’ll do their homework without complaining because of the rockstar status and then we’ll all live happily ever after.

Well, maybe not happily ever after. But at least through the car ride home.

Is that enough incentive to make these muffins? I mean, they use up the zucchini bats you have on your counter and they’re healthier and they’re filled with a cheesecake-like cream cheese filling.

Those are all good things, if you ask me.

Zucchini Cream Cheese Muffins - a fast and easy breakfast recipe!

These muffins are very easy to make. These muffins are the marriage of my zucchini bread recipe and my pumpkin cream cheese muffins. Turn the bread into muffins (they bake faster!) and then add a cheesecake-like cream cheese filling. The only difference between these muffins and the others is that the cream cheese is inside the muffin.

The cream cheese is a little surprise when you’re eating the muffins. Well hello, cheesecake-inside-muffins. What a pleasant surprise!

This recipe makes 12 hearty muffins. The batter for the zucchini bread comes together in one bowl and uses a hefty dose of applesauce instead of lots of butter or oil. They stay moist with a great texture, like you’d expect a muffin to be. The zucchini and cinnamon give the muffin a nice flavor that’s very similar to carrot cake. If you were so inclined, you could just replace the zucchini with carrot and poof, it would be like spring again.

The cream cheese filling is just two ingredients – cream cheese and sugar – and it’s spooned into the middle of the muffins when you layer the batters in the muffin tin. Simply bake, cool, and eat.

The other thing I love about muffins: they freeze well. They are perfect for quick mornings, or throw one in a lunchbox and it’ll be defrosted by lunch.

And your kid will loooove you for it!

Fast and easy Zucchini Cream Cheese Muffins! Perfect for leftover zucchini, these freeze well for easy breakfasts!

No yelling over lunches. Priceless!

Zucchini Cream Cheese Muffins

Zucchini Cream Cheese Muffins - these easy zucchini muffins are filled with a cream cheese mixture. Like eating a cupcake for breakfast, only healthier!
5 from 1 vote
Yield 12 muffins
Serving Size


  • 3/4 cup + 6 tablespoons granulated sugar divided
  • 1/4 cup vegetable oil
  • 1/4 cup unsweetened applesauce
  • 2 eggs
  • 7 tablespoons sour milk 1 teaspoon vinegar plus enough milk to make 7 tablespoons or you can use buttermilk
  • 1/2 teaspoon salt
  • 1 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 2 cups all purpose flour
  • 2 cups shredded zucchini
  • 4 ounces cream cheese softened


  • Preheat oven to 350°F. Line muffin cups with liners or spray with cooking spray.
  • Stir 3/4 cup sugar, oil, and applesauce in a large bowl with a wooden spoon or spatula. Stir in eggs, milk, salt, baking soda, and cinnamon. Slowly stir in flour, then stir in zucchini.
  • In a separate bowl, stir cream cheese and 6 tablespoons sugar until smooth.
  • Place about 2 tablespoons of batter in the bottom of each of 12 muffin cups. Top with equal portions of cream cheese (about 1 tablespoon per muffin) then equally divide remaining muffin batter over the top.
  • Bake for about 18-24 minutes until the muffins are golden brown. Cool before eating. Serve warm or cold! Store in an airtight container for up to 3 days for freeze for up to 1 month.

Nutritional information not guaranteed to be accurate

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44 CommentsLeave a comment or review

  1. Just made these, but I think they need baking powder or soda, there no fluffy consistentsy. Do you put either of those in your recipe? 

      1. Just seeing this. Oh thanks! I was so disappointed bc I had to throw them all out, and cream cheese doesn’t come cheap and it’s not something I always have on hand . Thanks for responding! If I get around to making them again I’ll make sure to let you know how they turn out. 

    1. Just seeing this. Oh thanks! I was so disappointed bc I had to throw them all out, and cream cheese doesn’t come cheap and it’s not something I always have on hand . Thanks for responding! If I get around to making them again I’ll make sure to let you know how they turn out. 

  2. I made these over the weekend for a BBQ party. I totally cut down on the sugar, used 2/3c. in the muffin and 3 T in the cream cheese, I think i could have cut it even more. They took a long time to cook, at least 30 minutes. The texture after they cooled was a bit weird I’ll admit very dense but they tasted yummy. The cream cheese did leak out the top so next time I’ll put 1 T muffin mixture first then 1 T cream cheese then 2T more on top to help keep the mixture in. I also forgot buttermilk, so I used 1 cup almond/coconut milk with 1T lemon juice, let it sit for 5 minutes and just used what I needed. Had several people comment on how good they were. Thanks!

  3. These are delicious, the recipe is a keeper for sure. Thanks for sharing it!
    There’s still a point I’d like to bring though: I’m really not sure why there would be 6 tablespoons of sugar in 1/2 cup of cream cheese. I only put 2 tablespoons of sugar and it was sweet enough.
    Also, I modified the recipe a bit to fit my breakfast needs: I changed the white flour for some wheat and other grain flours (I don’t remember which ones). Finally, I subsituted half the zucchini for carrots because I didn’t feel like using all my zucchinis, which are quite expensive over here.
    Anyway, overall, lovely muffins. I truly like them!!!

    1. I’ve never used almond/coconut flour, so I’m not sure how they interchange with AP. If you’re looking to make it GF, you can use Bob’s Red Mill 1:1 flour for substituting!

  4. You are officially my first recipe comment of the thousands I have read and few I have actually tried. I used this recipe, although WITHOUT the cream cheese part, to make whoopie pies! It made exactly 12 perfect pies using a whoopie pie pan. I used a different recipe than yours for the cream cheese filling but the cakes are fantastic especially using unsweetened applesauce in lieu of butter! It only took one large zucchini to make the whole 2 cups and it’s even better that it is Not required to extract the zucchini liquid! I gave these whoopie pies to my Meals on Wheels clients and they were a hit! I’ll be sharing this for sure!