These lemon poppy seed cupcakes are tender and moist thanks to the addition of grated zucchini! Topped with easy cream cheese frosting, they are naturally sweetened and lower in natural sugar than most cupcake recipes. The perfect treat for any celebration!

A zucchini lemon poppy seed cupcake with a bite taken out of it. More cupcakes are next to it on the table and cooling rack.

A few summers ago, a friend of mine mentioned how much she loved the flavor combination of zucchinis and lemon.

Say wha? That was a veggie-loaded combo I hadn’t tried and you best believe that when the end-of-summer crazy zucchini harvest happened, I was all over trying out that flavor mix.

And, TNNers, my dear friend was spot on and my super popular Healthy Zucchini Lemon Muffins were born.

But as another summer comes to an end, the gardens are once again bursting with zucchinis that need a purpose, and my inbox is flooded with requests from you all for healthier dessert recipes….I now bring you Zucchini Lemon Poppy Seed Cupcakes.

Love the idea of veggies making your desserts a little better? Check out my Beetroot Chocolate Cake and be dazzled!

Process images of how to make the batter for these zucchini lemon poppyseed cupcakes

Why these lemon cupcakes are edible magic

  • The grated zucchini in this lemon cupcake recipe not only adds a great flavor, but makes these little cakes perfectly moist!
  • Healthier than traditional cupcake recipes, as these cupcakes are naturally sweetened with maple syrup or honey AND they have about half of the sweetener of most recipes out there.
  • Flavorful and tender. These cupcakes might be healthier, but they don’t skimp on the yum factor!
  • Adaptable. I get that we all have different needs and/or preferences when it comes to food, so just like most of my recipes, these lemon poppy seed cupcakes can be adjusted to fit your style of eating. Check out the suggested adaptations section below.
  • This recipe is crazy easy to make!

Like many awesome things in life, this healthy cupcake recipe came to be out of two people putting together their greatness! My dear friend and fellow blogger, Heather Staller, helped me test and develop this lemon poppy seed cupcake recipe. Between the two of us, we have hit cupcake perfection!

Suggested Adaptations

  • Make these lemon poppy seed cupcakes gluten free. You can use a cup-for-cup style gluten free flour mix instead of the regular flour. I like this brand.
  • Make these cupcakes egg-free. Since this recipe has one egg, you can easily substitute a flag “egg” or other liquid egg substitute.
  • Need dairy-free? Use a dairy-free, plain yogurt or sour cream such as a coconut-based or other plant-based yogurt.
  • Skip the poppy seeds. You can simply leave them out if you don’t like them or don’t have them on hand.
  • Use yellow summer squash instead of zucchini in this lemon cupcake recipe. Just grate it up and squeeze out the moisture and add to the recipe just as you would the zucchini.
  • Not a cream cheese fan? You can top these lemon poppy seed cupcakes with a simple lemon glaze (recipe below).

Easy Lemon Glaze

I topped these zucchini lemon poppy seed cupcakes with a simple cream cheese frosting because they are not overly lemony and the creamy tang of the cream cheese was a heavenly pairing. I also love that I could easily keep this cupcake recipe refined sugar-free with the cream cheese frosting.

However, if cream cheese isn’t your thing, you can easily make a lemon glaze to top these zucchini cupcakes!

  • 1 cup powdered sugar
  • 2 to 3 Tablespoons fresh lemon juice
  1. For lemon glaze, mix the powdered sugar with a little lemon juice a little at a time until you get a thick glaze consistency. If you add too much lemon juice and the glaze is too thin (runs off the cupcake), add a tablespoon of powdered sugar or more until it gets to the right consistency.
  2. Dip the top of each cupcake into the glaze or drizzle the glaze on top with a spoon.
  3. Serve right away or leave at room temperature, uncovered, for up to 6 hours.

This recipe is…

Vegetarian and refined sugar-free. It is easily gluten free and egg-free with adaptations (see above).

Other dessert recipes that you are going to adore…

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A zucchini lemon poppy seed cupcake with a bite taken out of it. More cupcakes are in the background.
5 from 2 votes

Zucchini Lemon Poppy Seed Cupcakes

Yield: 12 cupcakes
Prep Time: 15 minutes
Cook Time: 20 minutes
Cuisine: American
Course: Dessert
These lemon poppy seed cupcakes are tender and moist thanks to the addition of grated zucchini! Topped with an easy cream cheese frosting, they are naturally sweetened and lower in natural sugar than most cupcake recipes. The perfect treat for any celebration!


Zucchini Lemon Poppy Seed Cupcakes

  • 2 cups white whole wheat flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ¼ teaspoon salt
  • 2 tablespoons poppy seeds
  • 1 ½ cups grated zucchini
  • 1 large egg
  • ½ cup unsweetened applesauce
  • ¼ cup avocado oil, or neutral tasting oil
  • ½ cup honey or maple syrup
  • 1/3 cup plain Greek yogurt
  • 2 lemons, zested
  • 3 tablespoons lemon juice
  • 1 teaspoon vanilla extract

Easy Cream Cheese Frosting

  • 1 cup whipped cream cheese
  • 3-4 tablespoons honey or maple syrup, or to taste
  • 1/2 teaspoon vanilla extract


  • Muffin tin


Zucchini Lemon Poppy Seed Cupcakes

  • Preheat the oven to 350℉. Line a standard muffin tin with paper liners or grease well with extra oil.
  • In a medium-sized bowl add the flours, baking powder, baking soda, salt, and poppy seeds. Whisk together to combine.
  • Place grated zucchini in a clean kitchen towel or a few layers of paper towel and squeeze out all of the excess liquid. Place dry zucchini into a large bowl. Add the remaining ingredients and whisk to combine.
  • Dump the flour bowl into the wet ingredients and stir with a large spoon or spatula until no dry flour remains.
  • Divide the batter evenly between the muffin cups. Bake until lightly golden brown on the top and cooked through, 18-20 minutes. Allow to cool for 5 minutes in the pan then transfer the cupcakes to a cooling rack to cool completely before frosting.
  • Once cupcakes are cool, frost as desired or right before enjoying. Unfrosted, cupcakes can be stored in an airtight container at room temperature for a day or refrigerated for 3 days.

Easy Cream Cheese Frosting

  • Mix cream cheese, honey/maple syrup , and vanilla in a bowl until smooth.
  • Spoon a dollop of the frosting on top of each cupcake then spread evenly with the back of the spoon or a small spatula.
  • Enjoy right away or refrigerate for up to 24 hours.
Serving: 1cupcake, Calories: 262kcal, Carbohydrates: 35g, Protein: 6g, Fat: 13g, Saturated Fat: 4g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 5g, Trans Fat: 1g, Cholesterol: 37mg, Sodium: 247mg, Potassium: 160mg, Fiber: 3g, Sugar: 19g, Vitamin A: 315IU, Vitamin C: 14mg, Calcium: 91mg, Iron: 1mg
Nutritional information provided here is only an estimate shared for convenience and as a courtesy. Information will vary based on ingredients + brands used to create the recipe.