Zucchini Muffins with Cream Cheese Filling

08 September 2018 by Natanja

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  • Tall, soft and fluffy zucchini muffins with cream cheese filling.

    Zucchini muffins filled with cream cheese next to a butter knife and cinnamon sticks.

    Is there anything better than a tall fluffy soft muffin that looks like it came straight from the bakery, filled with flavors of cinnamon, nutmeg and with just the right amount of sweetness? YES! A tall fluffy soft muffin with a cream cheese center. Yes please!

    Up till a months weeks ago I have never filled anything with cream cheese. (I know, shocking!) Until recently cream cheese was just a spread I used on a piece of toast or as a main ingredient in a cheesecake. But after spontaneously deciding to try to swirl it into a banana bread, my world has forever changed! And after discovering this magical way to transform ordinary baked goods into clouds of heaven I have two questions.

    1. Why are we still making quick breads without cream cheese centers?
    2. Who came up with this genius idea and how can I reach them to say thank you?!

    No but seriously stuffing things with cream cheese makes them extra yummy. That wonderful tangy taste of the slightly sour cream cheese goes together so incredibly well with the sweet muffin. The center kind of reminds you of cheesecake which makes these muffins taste like a muffin and a cheesecake just had a baby. Lovely thought, isn’t it? 😉

    Zucchini muffins filled with cream cheese next to oats and egg shells.

    Sky High Muffins

    I have made these muffins a total of 4 times before finding just the right ratios. I also learned a few new things in the process just like this amazing trick for getting sky high muffins without them sinking once you take them out of the oven. The trick is to bake them at a high temperature (200C or 390F) for 5 minutes and then turn down the temperature to 180C or 350F and bake them until they are done. This creates a lovely high and fat muffin just like the ones you see in the windows of bakeries.

    (This trick only works with thicker kinds of batters so be aware if you wish to try this out on a different recipe.)


    For grating the zucchini you want to use the finer side of the grater and grate them into small flakes (or specs or strands or whatever you want to call it). Smaller pieces don’t just look better, they also make the muffins bake better as you are working with a more uniform batter. You do not need to squeeze out the water of the grated zucchini. Simply toss it into the bowl with your wet ingredients.

    Soft Muffins

    To ensure that your muffins turn out delicious, you need to work with room temperature ingredients. This is vital for ensuring that the muffins bake correctly. I know that this step is a bit annoying if you wish to bake muffins straight away and don’t want to wait until your ingredients come to room temperature. But it’s really important, trust me! Also be sure to not over mix your batter once you combined the wet ingredients with the dry. This will result in a tough muffin. Simply mix them together with a spatula until no more flour specs remain. Voilà.

    A closeup of the zucchini muffins filled with cream cheese on brown parchment paper.

    Baking Time

    Because ovens are all so different there is no way to give an exact baking time. Check on your muffins after 18 minutes and then again every 2 minutes to avoid over baking them. Since these muffins have a cream cheese center, you cannot stick a toothpick into the center to test if they are done. If the tops look done and you have baked them for at least 18 mintues, you are good to go. You can also try gently pressing the tops a bit and seeing if they are still doughy (careful hot!).

    If you give these zucchini muffins a try, let me know in the comment section down below how you liked them. I always love hearing from you!

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    A closeup of a sliced muffin showing the cream cheese center

    Zucchini Muffins with Cream Cheese Filling

    • Prep Time: 15 minutes
    • Cook Time: 18-20 minutes
    • Total Time: 35 minutes
    • Yield: 12 1x


    Tall, soft and fluffy muffins with a tangy cream cheese filling.



    Zucchini Muffins

    • 240g flour (2 cups)
    • 1 teaspoon baking powder
    • 1/2 teaspoon baking soda
    • 1/8 teaspoon salt
    • 1 and 1/2 teaspoons cinnamon
    • 1/4 teaspoon nutmeg
    • 200g white granulated sugar (1 cup)
    • 100ml oil (1/2 cup)
    • 60ml milk (1/4 cup), room temperature
    • 2 eggs, room temperature
    • 1 teaspoon vanilla extract
    • 125g finely grated zucchini (1 cup)

    Cream Cheese Filling

    • 110g cream cheese (1/2 cup), room temperature
    • 2 tablespoons white granulated sugar
    • 1/2 teaspoon vanilla


    1. Preheat the oven to 200C or 400F and spray a 12-count muffin tin with nonstick spray.
    2. In a medium bowl, combine flour, baking powder, baking soda, salt, cinnamon and nutmeg. Whisk until everything is well combined.
    3. In a seperat bowl, whisk together the sugar and oil. Add in the milk, eggs and vanilla and continue mixing until well combined. Then fold in the grated zucchini.
    4. Pour the wet ingredients into the dry and fold everything together with a spatula just until no flour specs remain.
    5. For the cream cheese filling, combine all the ingredients together, stirring until smooth.
    6. Fill the muffin tins with 1 tablespoon batter, then add 1 teaspoon cream cheese filling on top and cover with batter until tins are 3/4 full.
    7. Bake for 5 minutes at 200C (400F) and then turn the temperature down to 180C (350F) and bake for an additional 13-15 minutes. Muffins should be done after 18-20 minutes total.
    8. Let them cool before removing them from the muffin tin.


    Store cupcakes in an airtight container for up to 2 days at room temperature or up to 5 days in the fridge. Or freeze, wrapped tightly with plastic wrap and stored in a ziplock bag, for up to 3 months.

    Cream cheese stuffed zucchini muffins next to a green zucchini and a butter knife


    Disclosure: This post may contain affiliate links, but these are all products I highly recommend. I won’t put anything on this page that I haven’t verified and/or personally used.

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