These Cream Cheese Zucchini Muffins are a wholesome twist on a bakery favorite, combining fluffy spiced zucchini batter with a rich, creamy cheesecake center.
Naturally moist from fresh zucchini, they’re packed with fiber, plant-based nutrients, and healthy fats, making them both satisfying and nourishing.
With less saturated fat than typical muffins, these treats are perfect for everyday snacking, quick breakfasts, or meal prep—balancing indulgence and nutrition in every bite.
Cream Cheese Zucchini Muffins
Equipment
- 1 × 12-cup muffin pan
- 10 × paper muffin liners (or nonstick spray)
- 2 × mixing bowls (large and medium)
- 1 × handheld or stand mixer
- 1 × whisk
- 1 × spatula
- 1 × grater (for zucchini)
Ingredients
For the Muffin Batter:
- 1 ½ cups 188 g all-purpose flour
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- 2 teaspoons ground cinnamon
- ¼ teaspoon ground nutmeg
- ½ cup 120 ml vegetable or canola oil
- ¼ cup 50 g packed light or dark brown sugar
- ½ cup 100 g granulated sugar
- 1 large egg room temperature
- 1 teaspoon vanilla extract
- 1 ¼ cups 150 g shredded zucchini (unpeeled, unblotted)
- Optional: coarse sugar for topping
For the Cream Cheese Filling:
- 5 oz 142 g full-fat brick cream cheese, softened
- 1 egg yolk room temperature
- ½ teaspoon vanilla extract
- 3 tablespoons 36 g granulated sugar
Instructions
- Prepare the oven and pan: Begin by preheating your oven to 425°F (218°C). This high starting temperature helps the muffins rise quickly, creating tall, bakery-style domes. While the oven heats, take out a 12-cup muffin pan and either line 10 of the cups with paper muffin liners or lightly coat them with nonstick spray. This recipe makes about 10 muffins, so a couple of the cups will remain empty. Preparing your pan first ensures that the batter can be filled and baked immediately once mixed, preventing the leavening agents from losing strength.
- Combine the dry ingredients: In a large mixing bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg. Stir until the mixture looks uniform and the spices are evenly distributed throughout the flour. This step prevents clumps of baking powder or spices, which could cause uneven flavor or texture in the finished muffins. Setting this bowl aside now makes it easy to fold everything together later without overmixing.
- Mix the wet ingredients: In a separate medium-sized bowl, add the oil, brown sugar, and granulated sugar. Whisk them together until the mixture is smooth and glossy, with no visible sugar lumps. Next, crack in the egg, pour in the vanilla extract, and whisk again until the mixture is thoroughly blended. Finally, stir in the shredded zucchini, which adds natural moisture and fiber. You don’t need to blot the zucchini dry; its moisture is key to the muffin’s soft texture. At this point, your wet mixture should look thick but pourable, with flecks of green zucchini throughout.
- Combine wet and dry mixtures: Pour the wet zucchini mixture into the large bowl of dry ingredients. Using a whisk or spatula, gently stir the two together until just combined. The batter should look slightly lumpy, which is a good sign—it means you haven’t overmixed. Overmixing muffin batter can develop too much gluten in the flour, resulting in tough, dense muffins. Stop stirring as soon as the streaks of flour disappear. Your batter is now ready to layer with the cream cheese filling.
- Prepare the cream cheese filling: In another medium bowl, add the softened cream cheese and beat it using a handheld or stand mixer on medium-high speed until smooth and creamy. This ensures no lumps of cream cheese remain. Add the egg yolk, vanilla extract, and granulated sugar. Continue beating until everything is evenly combined and the mixture looks silky and thick. This filling will bake into a luscious cheesecake-like center inside each muffin, creating a delightful contrast to the spiced zucchini batter.
- Layer the muffin cups: Spoon one heaping tablespoon of muffin batter into each prepared muffin cup, spreading it slightly so it covers the bottom. Next, add one tablespoon of the cream cheese filling directly on top of the batter. Finally, top each with another heaping tablespoon (or enough to fill the cup nearly to the rim) of muffin batter. Some cream cheese may peek out from the top or sides—this is perfectly fine and adds character to the muffins. If desired, sprinkle a pinch of coarse sugar on top of each muffin for a crunchy bakery-style finish.
- Bake at two temperatures: Place the pan in the preheated oven and bake for 5 minutes at 425°F (218°C). This initial high heat encourages the muffins to rise quickly, creating tall, domed tops. Without removing the muffins from the oven, reduce the temperature to 350°F (177°C) and continue baking for 15–17 minutes. The total baking time should be around 20–22 minutes. You’ll know the muffins are done when the tops are golden brown and a toothpick inserted into the muffin part (not the cream cheese filling) comes out clean or with just a few moist crumbs.
- Cool before serving: Remove the pan from the oven and place it on a wire rack. Let the muffins cool in the pan for at least 10 minutes before carefully lifting them out. This short cooling period allows the muffins to firm up, making them easier to handle while keeping the centers creamy and soft. Serve warm for a gooey cheesecake center, or let them cool completely for a firmer texture.
- Store for later enjoyment: If you have leftovers, store them tightly covered at room temperature for up to 2 days, or refrigerate them for up to 1 week. For long-term storage, these muffins freeze beautifully—simply place them in an airtight container or freezer-safe bag and freeze for up to 3 months. To enjoy later, thaw overnight in the refrigerator and warm briefly in the microwave for a fresh-from-the-oven taste.
Notes
- Use freshly grated zucchini for the best texture and moisture—no need to peel or blot it dry.
- Full-fat cream cheese gives the smoothest filling and prevents a runny texture after baking.
- The two-temperature baking method ensures tall muffin tops and a bakery-style appearance.
- A sprinkle of coarse sugar adds crunch but is optional.
- Muffins freeze well and reheat beautifully, making them a great make-ahead treat.
Chef’s Secrets for Perfect Muffins
One of the keys to success with these muffins lies in the oven temperature trick.
Starting with a very hot oven gives the muffins their dramatic lift, while the lower temperature ensures the centers bake through without overbrowning.
Another secret is to avoid overmixing the batter; a few streaks of flour are fine, and the result will be lighter, softer muffins.
When preparing the cream cheese filling, beat it thoroughly so it is lump-free—this ensures a smooth, velvety center instead of one with small clumps.
Finally, measure flour correctly by spooning and leveling rather than scooping, as too much flour can make the muffins heavy.
Serving Suggestions for Every Occasion
These muffins are wonderfully versatile and can be enjoyed in many ways.
For breakfast, serve them slightly warm with fresh fruit or a cup of coffee for a balanced start to the day.
As a snack, they pair beautifully with a handful of nuts or yogurt.
If you’re entertaining, arrange them on a platter alongside savory options like cheese and olives to balance the sweetness.
They also make a thoughtful addition to lunchboxes since they hold up well at room temperature.
For a more indulgent dessert, try serving them with a drizzle of honey or a dusting of powdered sugar.
Storage Tips to Keep Them Fresh
Because these muffins contain cream cheese, proper storage is important for both safety and quality.
If you plan to enjoy them within two days, keep them covered at room temperature in a cool, dry spot.
For longer storage, refrigerate in an airtight container for up to one week; this keeps the filling fresh and prevents spoilage.
If freezing, wrap muffins individually in plastic wrap, then place them in a freezer-safe bag or container to prevent freezer burn.
They can be frozen for up to three months.
To serve, thaw overnight in the fridge and warm briefly in the microwave or oven to restore their soft texture.
Frequently Asked Questions
1. Can I use whole wheat flour instead of all-purpose?
Yes, you can swap half of the all-purpose flour for whole wheat flour for a nuttier flavor and added fiber.
However, using 100% whole wheat may make the muffins denser, so keeping part all-purpose ensures a softer texture.
2. Do I need to peel or squeeze the zucchini?
No, peeling isn’t necessary—the green skin adds color and nutrition. There’s also no need to blot or squeeze the zucchini dry, as the natural moisture is what makes the muffins tender and moist.
3. Can I make these muffins without cream cheese?
Absolutely! If you prefer a simpler zucchini muffin, just leave out the cream cheese filling and bake the batter as-is. You’ll get wonderfully moist spiced muffins, and you can add chocolate chips or nuts instead if you’d like.
4. Why start baking at a high temperature?
The initial high temperature helps the muffins rise quickly, creating tall, bakery-style domes. Once the heat is lowered, the insides continue to bake evenly without overbrowning.
This two-step process is a professional baking trick for picture-perfect muffins.
5. How can I tell when the muffins are done?
Insert a toothpick into the muffin portion (not the cream cheese filling). If it comes out clean or with just a few moist crumbs, the muffins are ready.
Be careful not to overbake, as this can dry out the batter even if the cream cheese looks soft.
