Zucchini Muffins may be subtly flavored, but they impart abundant moisture and a vibrant hue to baked treats. Zucchini muffins are tender, moist, and wonderfully spiced, making them a breeze to whip up. However, I believe there’s still room for enhancement.

To elevate the experience, these zucchini muffins boast a delightful cream cheese filling that is both sweet and tangy. Sink your teeth into the center of one of these muffins, and you’ll discover a luscious cheesecake pocket that will leave you questioning whether you’ll ever return to baking traditional zucchini muffins. They transcend the boundaries of breakfast or brunch and deserve a place among delectable desserts.

Tips for the Best Cream Cheese Zucchini Muffins

Creamy and tangy cream cheese adds an irresistible touch to any baked treat. Check out these helpful tips for creating perfect cream cheese-filled Zucchini Muffins.

  • For baking purposes, it is recommended to opt for cream cheese that is packaged in a brick rather than the one in a plastic tub. The latter has a distinct composition that allows for easier spreading, but it may not be the best choice for baking.
  • If you need to soften the cream cheese quickly, simply remove the packaging and place it on a microwave-safe plate. Microwave it in 10-second intervals until it reaches the desired softness.
  • To ensure that the cream cheese filling is evenly distributed, you can use a spoon or a butter knife to spread the batter and completely encase the filling. Alternatively, you can spread the cream cheese filling to the edges of the cups before adding the final layer of muffin batter. This will create a delightful swirled and layered effect in your muffins.

Skip the Cream Cheese Layer

If you want to make traditional zucchini muffins, just skip the cream cheese filling. Remember that without the filling, the recipe will make 9 to 10 muffins instead of 12. If you’d like to make a larger batch, you can double the recipe and make 18 muffins. Alternatively, you can try Elise’s amazing zucchini muffin recipe with walnuts and dried cranberries.

Baking with Zucchini

Zucchini is known for its mild and sweet flavor, which also adds moisture to baked goods. In many recipes, it is recommended to squeeze out the water from grated Zucchini Muffins. However, for these muffins, I decided to skip this step and keep the water in. As a result, the batter for these muffins is slightly thicker than usual, allowing it to handle the extra moisture.

I used regular zucchini from the grocery store. If you’re fortunate enough to have fresh zucchini from your garden, opt for the smaller ones as they tend to be less watery. To grate the zucchini, you can either use the coarse holes on a box grater or the grater attachment of a food processor.

How to Store and Freeze

If you find yourself with an abundance of Zucchini Muffins from your garden, don’t worry! You can save those muffins for later when you’re craving a taste of summer.

To freeze them, simply lay the baked and cooled muffins in a single layer on a baking sheet. Pop the sheet in the freezer for about 30 minutes, or until they’re completely frozen. Then, transfer the muffins into a freezer bag. They’ll stay fresh for up to three months in the freezer. Just remember to thaw them overnight in the refrigerator before enjoying.

clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon
Zucchini Muffins Recipe

Cream Cheese Zucchini Muffins

  • Author: Jeanine
  • Total Time: 40 mins
  • Yield: 12 muffins 1x


Try these delicious and nourishing Healthy Zucchini Muffins for a delightful treat. These muffins are filled with the goodness of zucchini, making them moist, tasty, and a clever way to incorporate some veggies into your daily routine. Whether you enjoy them for breakfast, as a snack, or as a surprise in your lunchbox, these muffins are sure to please everyone, regardless of age.



For the cream cheese filling

  • 6 ounces cream cheese, softened
  • 3 tablespoons granulated sugar
  • 1 teaspoon vanilla extract

For the zucchini muffins

  • 1 1/2 cups (180gall-purpose flour
  • 1 teaspoon baking powder
  • 1 teaspoon ground cinnamon
  • 1/2 teaspoon kosher salt
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon ground ginger
  • 1/2 teaspoon ground nutmeg
  • 1/2 cup (113gunsalted butter, melted
  • 1/3 cup (67ggranulated sugar
  • 1/3 cup (71g) packed light brown sugar
  • 1 large egg
  • 1 cup (about 180g) grated zucchini, packed
  • 2 tablespoons turbinado sugar, for sprinkling, optional


  1. Preheat the oven to 425°F.

    Position an oven rack in the center of the oven and preheat the oven to 425°F. Line a standard muffin pan with muffin liners.

  2. Make the cream cheese filling:

    In a small mixing bowl, whisk together the cream cheese, sugar, and vanilla extract until smooth and creamy, similar in thickness to peanut butter.

  3. Combine the dry ingredients:

    In a medium mixing bowl, whisk together the flour, baking powder, cinnamon, salt, baking soda, ginger, and nutmeg.

  4. Combine the wet ingredients:

    In a large mixing bowl, whisk together the melted butter, granulated sugar, and brown sugar until combined. Add the egg and whisk until it is fully incorporated. Stir in the grated zucchini until it is evenly distributed.

  5. Combine the wet and dry ingredients:

    Add the flour mixture to the zucchini mixture. Stir with a rubber spatula just until combined and no streaks of dry flour remain. The batter may seem slightly thicker than most muffin batters, but the zucchini will add a lot of moisture in the oven.

  6. Divide the batter:

    Use a cookie scoop or a couple of spoons to scoop a rounded tablespoon of batter into each muffin cup. Scoop a tablespoon of the cream cheese filling onto the batter. Divide the remaining muffin batter evenly between each muffin cup. You can use a spoon or a butter knife to ensure the batter completely encases the cream cheese filling or leave it be for more of a swirled layer.

    Sprinkle 1/2 teaspoon of turbinado sugar on the top of each muffin, if using.

  7. Bake:

    Bake the muffins for 5 minutes at 425°F, then reduce the oven temperature to 350°F and continue baking for about 15 minutes longer. When they’re fully baked, the tops of the muffins will be matte and the edges will have started to brown.

  8.  Cool the muffins and serve:

    Allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack to cool for at least 10 minutes more. Serve warm or at room temperature.

    Store cooled leftover muffins in an airtight container on the counter for up to 2 days or in the refrigerator for up to 1 week.

  • Prep Time: 20 mins
  • Cook Time: 20 mins
  • Category: Breakfast, Snack
  • Cuisine: American


  • Serving Size: 12 servings
  • Calories: 180 kcal
  • Sugar: 13g
  • Sodium: 185mg
  • Fat: 7g
  • Saturated Fat: 1g
  • Carbohydrates: 27g
  • Fiber: 2g
  • Protein: 4g
  • Cholesterol: 31mg

Keywords: zucchini muffins, zucchini muffins recipe, zucchini muffins healthy