Zucchini Cottage Cheese Muffins

Filled with whole grains and protein packed cottage cheese, these little muffins are a nutritious snack for toddlers and kids. Zucchini Cottage Cheese Muffins are egg-free and nut-free and can easily be made gluten-free as well.

Kids in the Kitchen:

  • What kiddo doesn’t love making muffins, right? Let your child put the paper liners in the muffin tin while you make sure you have all the other ingredients ready to go.
  • Zucchini: Having kids help prep the zucchini is great exposure to the veggie. Kids can wash and dry the zucchini, help trim the end with a safe knife, and then hold the zucchini with you as you grate it (or older kids can grate the zucchini on their own).
  • Measure and mix the dry ingredients: depending on the age or your child and/or how much time you have to bake, you may want to measure many of the ingredients before inviting your child to bake with you. You can leave a couple things for your child to measure, such as the baking powder and salt.
  • Toppings: If you’d like to use chocolate chips or blueberries in this recipe, kids can easily help press them into the top of each muffin.

Subs and Tips for Zucchini Cottage Cheese Muffins:

  • Cottage Cheese:  If you don’t want to see specs of cottage cheese in the muffins, you can blend it before using in the recipe. I often use an immersion blender to make it quick and easy. All cottage cheese brands are very different, so be aware that results of the muffins may vary depending on what kind of cottage cheese you use. My favorite it the low-fat Good Culture cottage cheese.
  • Flour: White whole wheat flour has a more mild taste than the traditional whole wheat flour. I like to buy the King Arthur brand. If you don’t have white whole wheat flour, use half regular whole wheat and half all-purpose flour to get similar results. You can also use all all-purpose flour if you prefer a more bakery-style tasting muffin.
  • Gluten-free?: Yes, no problem! I tested these muffins with a gluten-free “cup for cup” flour blend and it worked out really well.
  • Sweetener: I use coconut sugar and maple syrup for these muffins. You can use regular granulated sugar instead of the coconut sugar. Use less granulated sugar (measurements in recipe card) since it’s sweeter than coconut sugar. You can use honey in place of the maple syrup.
  • Helpful tools: Unbleached parchment paper liners, large cookie scoop (in picture below), and my favorite muffin tin are listed in my Baking Essentials list on Amazon HERE.

Zucchini Cottage Cheese Muffins

Healthy muffins packed with protein-rich cottage cheese, whole grains, and grated zucchini.
Prep Time 15 minutes
Cook Time 15 minutes
Total Time 30 minutes
Course Snack
Cuisine American
Servings 36 mini muffins or 12 large muffins


  • 1 medium-sized zucchini
  • 1 cup cottage cheese if your cottage cheese has large curds, you may want to blend it before using in recipe
  • 1/2 cup coconut sugar or 1/3 cup granulated sugar
  • 1/4 cup maple syrup
  • 1 tsp vanilla extract
  • 1/3 cup avocado or vegetable oil
  • 1/2 cup milk (any kind)
  • 2 cups white whole wheat flour or all-purpose or gluten-free blend
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp salt
  • 1/2 tsp cinnamon
  • 1/2 cup mini chocolate chips (optional)


  • Heat the oven to 375 degrees. Line a mini muffin tin (or standard size muffin tin) with paper liners or grease well.
  • Grate the zucchini on the smaller holes of a box grater until you have 1 1/2 cups of grated zucchini. Place the zucchini into a clean kitchen towel and squeeze out all of the excess moisture. You should have a full cup of grated zucchini after the liquid is squeezed out.
  • In a large bowl combine the grated zucchini, cottage cheese, sugar, maple syrup, vanilla, oil, and milk.
  • Add the flour then sprinkle over the baking powder, baking soda, salt, and cinnamon. (You could also whisk the dry ingredients together in a separate bowl first if you prefer.) Stir with a large spoon or spatula until everything is just combined. The batter will be thick, but try not to overmix or the muffins with be dense or tough.
  • Scoop the batter into the muffin tin, filling each hole about 3/4 of the way. Press some mini chocolate chips into the top of some or all of the muffins, if you'd like.
  • Bake until lightly golden brown on the top, 12 to 14 minutes for mini muffins and 16 to 20 minutes for standard muffins. Allow to cool fully before enjoying.
  • Muffins can be stored at room temperature for 2 days or refrigerated for 5 days. To freeze, wrap well and freeze up to 2 months.
Keyword cottage cheese, healthy kids snack, healthy muffins, zucchini

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Other Zucchini Recipes to try:

Zucchini Oatmeal Chocolate Chip Cookies

Easy Pesto Turkey Burgers

Zucchini Bread Bars



  1. Ashton on September 15, 2023 at 12:03 pm

    Could I add fresh or frozen blueberries instead of chocolate chips, or would that affect baking time?

    • Heather on September 17, 2023 at 4:54 pm

      Yes, you can add fresh or frozen blueberries without a problem.

  2. Lara on June 25, 2024 at 1:42 pm

    Could you make this with almond flour?

    • Heather on June 26, 2024 at 11:08 am

      No, unfortunately almond flour can not directly replace wheat flour. They absorb liquid very differently.

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