These Lemon Poppy Seed Muffins are tender, moist, full of lemon flavor and rocking an extra good-for-you ingredient…yellow squash! Made with white whole wheat flour, Greek yogurt, poppy seeds, and less added sugar than most muffin recipes, these muffins are packed with a cup and a half of grated summer squash! Mixed all in one bowl + done baking in under 20 minutes, these veggie-loaded muffins are a great grab-and-go choice for a healthy breakfast or tasty snack.

Lemon poppyseed muffin in a paper muffin liner. Lemons cut in half throughout image along with poppyseeds and crumbs on white countertop. Additional muffins and white plates out of focus in the background.

While zucchini is an old standby, you know I like to switch things up where I can (as evidenced by my NUMEROUS veggie muffin recipes). These yellow squash muffins use…you guessed it: yellow squash! Although almost an even swap flavor and texture-wise, baking with yellow squash helps even the most selective of eaters ease into veggie-loading as the color blends in almost seamlessly into these muffins. Sweetened with just enough brown sugar and applesauce and using white whole wheat flour for a lighter texture and flavor, these muffins still provide hearty staying power thanks to their added plant fiber and protein (from the Greek yogurt). A healthy helping of both lemon juice and zest give these nut-free muffins even more of a flavor boost.

Wanting more summer squash recipes? Check out my recipe links near the bottom of this post and try swapping yellow squash for the zucchini in my One-Bowl Healthy Oatmeal Carrot Muffins and Hearty Whole Wheat Banana Zucchini Muffins!

Individual white bowls of ingredients for yellow squash lemon poppyseed muffins. Two lemon halves, two individual yellow squash, and one egg sitting directly on white granite countertop.
Ingredients: grated yellow squash (summer squash), lemon zest, brown sugar, fresh lemon juice, egg or neutral tasting oil, plain Greek yogurt, unsweetened applesauce, avocado oil or other light flavored oil, vanilla extract, white whole wheat flour, baking powder, baking soda, salt, poppy seeds

How to make these yellow squash muffins: step-by-step visual guide

One hand holding a box grater and another hand grating yellow squash on the box grater. Box grater is sitting on top of white granite countertop.
Grate the summer squash.
Grated zucchini sitting in a white tea towel. Tea towel is sitting on top fo a white granite counter.
Place the grated summer squash on a tea towel or a few layers of paper towel.
Hand squeezing liquid out of grated yellow squash using a tea towel on top of a white bowl. White mixing bowl is sitting on top of a white granite counter.
Using either a tea towel or a few layers of paper towel, squeeze out all the excess liquid from the grated summer squash. Set aside.
Glass mixing bowl containing brown sugar and . Glass bowl is sitting on top of a white granite surface.
Place lemon zest and sugar in a large bowl.
Hand breaking up brown sugar in a glass mixing bowl. Glass bowl is sitting on top of a white granite surface.
Use your fingertips to rub the lemon zest and sugar together. This step is optional, but it helps bring out extra flavor in the zest.
Glass mixing bowl containing unmixed wet ingredients for yellow squash lemon poppyseed muffins. Glass bowl is sitting on top of a white granite surface.
Add in lemon juice, egg, yogurt, applesauce, oil, vanilla, and grated squash.
Glass mixing bowl containing yellow squash lemon poppy seed muffin batter. Whisk is sitting in the batter in the glass bowl. Glass bowl is sitting on top of a white granite surface.
Whisk together wet ingredients, brown sugar, and lemon zest.
Glass mixing bowl containing yellow squash lemon poppy seed muffin batter with flour on top of the batter. Glass bowl is sitting on top of a white granite surface.
Add flour to the wet ingredient mixture.
Glass mixing bowl with yellow squash lemon poppy seed muffin batter (ingredients unmixed). Glass bowl is sitting on top of a white granite surface.
Sprinkle the baking powder, baking soda, salt, and poppy seeds over the wet ingredient mixture.
Glass mixing bowl with yellow squash lemon poppy seed muffin batter. Glass bowl is sitting on top of a white granite surface.
Use a rubber spatula or large spoon to mix in the dry ingredients until just combined.
Hand holding onto cookie scoop, scooping muffin batter into 12 paper muffin tin liners in each section of a muffin tin.
Divide the batter evenly between the muffin cups.
Muffin tin filled with 12 yellow squash lemon poppyseed muffins. Half of a lemon and two yellow squash set aside on the edge of the image.
Bake until the muffins are light golden brown around the edges and no longer look wet in the center, 15 to 18 minutes.

What is the difference between yellow squash and zucchini? Turns out, not much! They both fall under the summer squash umbrella (along with varieties such as pattypan). Yellow squash tends to be a bit more crooked than zucchini and may have a few more seeds (all edible!). Other than that, they are pretty much interchangable in most recipes!

Suggested Adaptations

  • Toss in some blueberries for an extra summery muffin!
  • Replace the applesauce with mashed banana.
  • Make them gluten free: Use a cup-for-cup style gluten free flour mix instead of the whole wheat flour and make sure to use gluten free oats.
  • Need egg-free? I haven’t tested it, but I think using a common egg-replacer such a flax “egg” would work in this recipe.
  • Make them dairy-free by using your favorite plant based yogurt in place of the Greek yogurt.
  • Swap the yellow squash with zucchini. They are basically the same veggie, just different colors, and can be swapped out in most recipes…including these lemon muffins!

How to store these muffins

These muffins can hang out on your counter for a day, but if you plan to enjoy them over several days pop them in the fridge! Keeping them in an airtight container in your refrigerator will help to keep these moist muffins fresh longer and prevent molding.

You can also freeze these muffins for up to 2 months when stored in an air-tight freezer safe container. I like to thaw on the countertop overnight or by zapping one in the microwave for 15-30 seconds.

Lemon poppyseed muffins in paper muffin liners in a muffin tin. Lemon halves sitting on the muffin tin--out of focus are in the background of the image.

Other squash loaded recipes to try

Loving this Yellow Squash Lemon Poppy Seed Muffin recipe and now you’re hungry for more?

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One lemon poppyseed muffin stacked on top of another lemon poppyseed muffin (in a paper muffin liner). Lemons cut in half throughout image along with poppyseeds and crumbs on white countertop. Additional muffins and white plates out of focus in the background.
5 from 3 votes

Yellow Squash Lemon Poppy Seed Muffins

Yield: 12 muffins
Prep Time: 15 minutes
Cook Time: 20 minutes
Cuisine: American
Course: Dessert
These Lemon Poppy Seed Muffins are tender, moist, full of lemon flavor and rocking an extra good-for-you ingredient…yellow squash! Made with white whole wheat flour, Greek yogurt, poppy seeds, and less added sugar than most muffin recipes, these muffins are packed with a cup and a half of grated summer squash! Mixed all in own bowl + done baking in under 20 minutes, these veggie-loaded muffins are a great grab-and-go choice for a healthy breakfast or tasty snack.

Ingredients
 

  • 1 ½ cups grated yellow squash, (summer squash), measured before squeezing out.
  • 1 Tablespoon lemon zest, from 1-2 lemons
  • cup brown sugar
  • 3 Tablespoons fresh lemon juice
  • 1 large egg, or neutral tasting oil
  • cup plain Greek yogurt
  • ½ cup unsweetened applesauce
  • cup avocado oil, or other light flavored oil
  • 1 teaspoon vanilla extract
  • cups white whole wheat flour
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • 2 Tablespoons poppyseeds

Equipment

  • Muffin tin

Instructions
 

  • Preheat the oven to 375℉. Line a standard muffin tin with paper liners or grease well with extra oil.
  • Place grated squash in a clean kitchen towel or a few layers of paper towel and squeeze out all the excess liquid. Set aside.
  • Place lemon zest and sugar in a large bowl. Use your fingertips to rub the lemon zest and sugar together. This step is optional, but it helps bring out extra flavor in the zest.
  • Whisk in the lemon juice, egg, yogurt, applesauce, oil, vanilla, and grated squash.
  • Add the flour then sprinkle over the baking powder, baking soda, salt, and poppy seeds. Use a rubber spatula or large spoon to mix in the dry ingredients until just combined.
  • Divide the batter evenly between the muffin cups. Bake until the muffins are light golden brown around the edges and no longer look wet in the center, 15 to 18 minutes.
    If you have a kitchen thermometer, bake until the muffins have an internal temperature of 200℉. This will indicate that the muffins are baked through without over baking.
  • Allow to cool for 5 minutes in the pan then transfer the muffins to a cooling rack to cool for 15 minutes before enjoying.
  • Once completely cool, muffin can be stored in an airtight container at room temperature for 1 day or refrigerated for 3 days. You can also freeze your muffins for up to 2 months.
Serving: 1muffin, Calories: 153kcal, Carbohydrates: 19g, Protein: 4g, Fat: 7g, Saturated Fat: 1g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 5g, Trans Fat: 0.002g, Cholesterol: 16mg, Sodium: 140mg, Potassium: 99mg, Fiber: 2g, Sugar: 8g, Vitamin A: 54IU, Vitamin C: 5mg, Calcium: 68mg, Iron: 1mg