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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

Stack of Zucchini Cream Cheese Muffins

Zucchini Cream Cheese Muffins

5 from 4 votes
Zucchini Cream Cheese Muffins – these easy zucchini muffins are filled with a cream cheese mixture. Like eating a cupcake for breakfast, only healthier!
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
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  • 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.

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Recipe Nutrition

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
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 February 2, 2023

Dorothy Kern

Welcome to Crazy for Crust, where I share recipes that are sometimes crazy, often with a crust, and always served with a slice of life.

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  1. These are so yummy!! But my cream cheese came out and ran all over my oven 🙁 what did I do wrong?

    1. You may have over filled your muffin cups. I usually only fill cupcake pans with about 1/4 cup total of any batter – how much did you add?