Zucchini Cream Cheese Muffins

5 from 4 votes

These zucchini muffins have a hidden cream cheese center and are so easy to make. They taste like cupcakes but are healthier because they’re made with applesauce instead of lots of butter and oil!

These are freezer-friendly and great for breakfast, snacks or tuck them into your kid’s lunchbox for a noontime treat at school.

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

Are you looking for ways to use up all the summer zucchini? It gets a little out of hand this time of year! Well, you’re in luck because these easy muffins are the perfect way to use it up. In fact, you might not need any other recipes because once you try these zucchini cream cheese muffins you’ll be hooked.

This is an old favorite recipe of mine that I’ve been making for years. These muffins taste like cupcakes, but they’re a lot healthier and loaded with zucchini. It’s the cream cheese center that makes them feel like a dessert, but you can serve them for breakfast, brunch, or as a snack.

These are the Best Zucchini Bread Muffins!

  • Hello, one-bowl muffin recipe!
  • They’re a little lighter thanks to applesauce in the batter.
  • They have a hint of cinnamon.
  • They are tender and moist and freeze really well! 

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 filling. 

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

How to Add Zucchini to Muffins

Want to know a secret? You can’t taste the zucchini in these muffins but you can see the pretty green flecks when you take a bite.

So, why add it? I’m glad you asked – zucchini adds lots of moisture to baked goods, so it makes them even better. 

It’s very easy to add it to the muffins. Shred your zucchini either with a box grater or with a food processor. Once you’ve made the batter you just fold the shredded zucchini in at the end. 

Moist Zucchini Muffins with Cream Cheese Filling

This recipe makes twelve hearty muffins. You only need one bowl to make the batter and, like I mentioned, applesauce takes the place of some of the oil so they’re a little lighter and healthier.

They have an amazing texture and are really moist. The moisture comes from the shredded zucchini and applesauce so they stay moist for a few days even if they’re stored at room temperature.

They actually remind me a lot of carrot cake except healthier. In fact, you could substitute the zucchini for carrots and it would be like a healthier carrot cake muffin with that little dollop of cream cheese inside.

How to Make Muffins with Cream Cheese Filling

Once you’ve made the muffin batter spoon about two tablespoons of it for each muffin cup.

For the cream cheese filling (which is just softened cream cheese mixed with sugar), just spoon about a tablespoon of it into each cup. Center it on the muffin batter and then, cover it with more muffin batter.

The filling will stay tucked in the muffin while it bakes so you get a taste of creamy sweet cheesecake in every bite.

They are delicious served warm, but equally good served cold, too! I love to tuck them in Jordan’s lunches so she has a special treat at lunchtime.

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

These Zucchini Muffins are Freezer-Friendly

Pretty much at the end of each summer, when I have a pile of zucchini on hand, I make batches of these muffins and freeze them. They keep well for two to three months in the freezer!

  • Be sure to let them cool fully before freezing them.
  • I like to wrap them individually and then store them in a freezer bag. It makes it really easy to pull them out a few at time when we want one.
  • You can thaw them in the fridge, at room temperature, or just pop one in the microwave. For lunches, I usually put them in the lunch bag frozen and they are thawed by lunchtime.

This is a tried and true zucchini muffin recipe, friends! You know I won’t steer you wrong, so make time to make a batch of these little treats. You will love how easy and how delicious they are – enjoy!

Other Zucchini Recipes

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 4 votes
Prep Time 30 minutes
Cook Time 20 minutes
Total Time 50 minutes
Yield 12 muffins
Serving Size 1 muffin


  • 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 ¾ 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.

Nutrition Information

Serving: 1muffin | Calories: 218kcal | Carbohydrates: 31g | Protein: 4g | Fat: 9g | Saturated Fat: 6g | Cholesterol: 39mg | Sodium: 235mg | Potassium: 115mg | Fiber: 1g | Sugar: 14g | Vitamin A: 222IU | Vitamin C: 4mg | Calcium: 31mg | Iron: 1mg

Nutritional information not guaranteed to be accurate

Course Breakfast
Cuisine American
Keyword muffin, zucchini
collage of zucchini muffins photos

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Fast and easy Zucchini Muffins! Perfect for leftover zucchini, these freeze well for easy breakfasts! This delicious muffin recipe is full of cream cheese making these zucchini cream cheese muffins with a surprise inside.

Last Updated on August 7, 2020

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48 CommentsLeave a comment or review

  1. 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!

    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!

  2. 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!!!

  3. 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!

    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. 

  4. 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. OMG! Thank you. I’m so sorry! I can’t believe I forgot that, it’s totally in my notes. 🙁 It’s edited now, thank you again! 1 teaspoon of baking soda. 🙂

      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. 

  5. Love the cream cheese filling! Perfect way to use up the abundance of zucchini right now!

  6. No kiddos here but I am totally packing these for ME! That cream cheese center is calling my name!!