Zucchini Lemon Poppy Seed Cupcakes
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 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 Healthfy 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!

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!


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 flax “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
- 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.
- Dip the top of each cupcake into the glaze or drizzle the glaze on top with a spoon.
- 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).
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Zucchini Lemon Poppy Seed Cupcakes
Ingredients
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
Equipment
- Muffin tin
Instructions
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.


I just discovered your website and we made your chocolate beetroot cake with raspberry whipped cream for my birthday recently. It was delicious! So moist and flavorful, not too sweet, and leaves you feeling good after eating it. Will definitely make it again and try it as cupcakes for a kid birthday party along with your sweet potato frosting. I’m thinking to make this lemon poppy seed zucchini cupcake recipe as well for that birthday so the kids have some options.
I used regular whole fat yogurt for the chocolate beetroot cake because my Greek yogurt was low-fat. Do you recommend whole fat yogurt for these recipes or do you think low-fat Greek yogurt would work okay?
Thank you so much for sharing these recipes. Your website is a wonderful resource and I will be passing it along to others!
Hi Laila! So glad you are enjoying my recipes! While full fat dairy certainly gives baked goods a lovely richness, I find that low fat works just as well. If I feel like a certain fat content of an ingredient is important to the success of a recipe, I note it in the recipe card!
Love your recipes! Thank you for sharing them! On the poppy seed lemon cupcakes, can I use sesame seeds instead?
Sesame seeds have a very different flavor. If it is a flavor you enjoy, you can try but the end result will taste different then what I tested!
These are AMAZING!! Truly pillowy and moist and tender! I didn’t have poppyseeds or lemons so I added some nutmeg, and the yoghurt I used was fat free. I chose the honey option. The only place I really differed was the amount of zucchini. I shredded two and ended up with two big cups of it, and so I thought to myself, what am I going to do with half a cup of shredded zucchini…. well, it’s probably fine! And I dumped it all in. lol This could be why it took 30 minutes to fully bake. In hindsight, I could have put it in the fridge for tomorrow’s scrambled egg.
Recently my husband found out his cholesterol is shockingly high so I’ve pivoted my cooking to go hardcore low in saturated fat. We were already eating pretty healthy, so it’s just a matter of finding ways to slash saturated fat. I’ve printed off a few of your recipes to try so he has something more exciting than carrots to eat. This was the first on my list, and it was such a success that I’m adding it to my permanent repertoire! I’m looking forward to trying the rest.
Thank you for this great recipe!!
Oh I am so glad you enjoyed them so much, Julie!
Excellent, light, beautiful texture & flavor! I didn’t have applesauce so I used an additional 1/2 cup grated zucchini. That may have impacted the sweetness level, they are still great to me.
Oh so glad you loved them so much! Thank you for coming back and sharing, Minda!