Skip to Content

Yellow Squash Muffins with Lemon & Poppy Seeds

These Yellow Squash Muffins are a new riff on traditional lemon poppy seed muffins. Shredded summer squash adds lots of moisture and nutrition to the muffins. And that sweet-tart lemon glaze on top? Oh my!

lemon poppy seed squash muffins

There are only 13,000,000 internet search results for “Yellow Squash Muffins”, as opposed to the 26,000,000 results for “Zucchini Muffins”.  I know because I Googled it. So it looks like the world needs a yellow squash muffin recipe, no?

Well, maybe the world doesn’t need just another squash muffin recipe, but this recipe has lemon zest, crunchy poppy seeds and a sweet/tart lemony glaze to make them extra special. This recipe is one in 13,000,000, if I do say so myself.

Scroll through the step by step photos to see how to make Yellow Squash Muffins with Lemon & Poppy Seeds:

shredded yellow squash in a paper towl

Layer the shredded squash between layers of paper towels to wick away excess moisture.


adding poppy seeds to muffin batter.

Soak the poppy seeds in milk before adding them to the batter.


scooping muffin batter into the pan

A scooper makes portioning the batter very easy.


glazing a lemon poppy seed squash muffin

Dip the warm muffins into the lemon glaze.


a glazed yellow squash muffin

Allow the excess glaze to drip back into the bowl


glazed lemon poppy seed muffins on a rack

The glaze will set as the muffins cool.

Of all my zucchini recipes, I’m particularly crazy about my Chocolate Orange Zucchini Bread. So that recipe was the starting point for this new version of lemon poppy seeds muffins.

How I turned zucchini bread into Yellow Squash Muffins:

  • Obviously, I used yellow squash instead of zucchini. That’s an easy 1:1 trade off since both veggies have the same texture and water content.
  • As I do whenever I bake with zucchini, I layered the shredded squash with paper towels to absorb excess moisture.
  • I eliminated the cocoa from the original recipe and replaced it with an equal amount of flour. 
  • Inspired by the lemony-yellow color of the squash, I ditched the spices in the original recipe and added lemon zest and poppy seeds for a different flavor profile.
  • Finally, I created a sweet/tart lemon glaze to top the muffins. You can leave it off if you want a lower sugar muffin.

Do you need to soak poppy seeds in milk before baking?

If you’ve ever made a poppy seed cake or muffin you’ve probably seen the instruction to soak the poppy seeds in milk or water.

A while ago, as I was testing the recipe for my Triple Citrus Poppy Seed Cake I did a little kitchen experiment.

I was wondering if it was really necessary to soak the poppy seeds before adding them to the batter. I wanted to know if it really makes any difference to the taste or texture of the cake.

Spoiler alert! I obviously decided it was worth the time since I included the step to soak the poppy seeds in this recipe.

Go ahead and click over to the Triple Citrus Poppy Seed Cake post so you can read about my experiment. Sometimes these little steps do make a difference.

lemon poppy seed squash muffins

lemon poppy seed squash muffins

It’s amazing how just a few simple changes to one recipe can yield two very different, yet equally delicious, treats. Once again proving that baking is both an art and a science.

Want more muffin recipes? Bacon & Egg Muffins, Blueberry Cornbread Muffins, Sourdough Blueberry Muffins, Sunflower Muffins, Zucchini Muffins, Bran Muffins, Cranberry Orange Muffins, Lemon Blueberry Muffins.

If you love this recipe as much as I do, I would really appreciate a 5-star review.

lemon poppyseed squash muffins
Print Recipe
4.56 from 18 reviews

Yellow Squash Lemon & Poppy Seed Muffins

A new riff on everyone’s favorite lemon poppy seed muffin. Shredded summer squash adds lots of moisture and nutrition to the muffins.
Prep Time30 minutes
Bake Time15 minutes
Total Time45 minutes
12 muffins


  • 2 ½ oz poppy seeds (½ cup)
  • 4 oz whole milk (½ cup)

Muffin Batter

  • 16 oz yellow squash (2-3 medium)
  • 10 oz all-purpose flour (2 cups)
  • 1 ½ teaspoons baking powder
  • ½ teaspoon salt
  • 8 oz granulated sugar (1 cup)
  • 1 ¾ oz vegetable oil (¼ cup)
  • 3 large eggs
  • 2 lemons (zest very finely grated)
  • ½ teaspoon lemon extract


  • 4 oz confectioner’s sugar (1 cup)
  • 1 ½ oz fresh lemon juice (3 tablespoons)


  • Place2 ½ oz poppy seeds in a small bowl and pour 4 oz whole milk over the seeds. Set aside to soak for at least 1 hour and up to 3 hours.
  • Preheat the oven to 350 °F. Butter and flour a 12 cup muffin pan or line with paper cupcake liners.
  • Use the large holes of a box grater or the large grating disc of a food processor to shred 16 oz yellow squash. Spread the squash in an even layer on a paper towel and cover with another paper towel. Press to absorb the liquid. Let the squash sit while you mix the batter.
  • Combine 10 oz all-purpose flour, 1 ½ teaspoons baking powder, ½ teaspoon salt and 8 oz granulated sugar in a mixing bowl and whisk to combine.
  • In another bowl, whisk together 1 ¾ oz vegetable oil and 3 large eggs. Stir the squash, finely grated zest from 2 lemons and ½ teaspoon lemon extract into the wet ingredients.
  • Add the wet ingredients to the dry ingredients all at once and stir just until combined. Drain and rinse the poppy seeds and fold them into the batter.
  • Use a 2 ounce scooper or 1/4 cup measure to portion the batter into the prepared pan. Bake until the muffins spring back when lightly pressed in the middle, 12-15 minutes
  • While the muffins bake, combine 1 ½ oz fresh lemon juice and 4 oz confectioner’s sugar to make the glaze.
  • Cool the muffins in the pan for 5 minutes. Lift each still-warm muffin from the tin and dip the top into the lemon glaze. Set on a cooling rack. The glaze will set as the muffins cool.


My Book
Kitchen Scale
KA Stand Mixer
Food Processor
Muffin Pan

As an Amazon Associate and member of other affiliate programs, I earn from qualifying purchases.


This recipe will also make 6 jumbo muffins or one 9"x5" loaf. Adjust the baking times as needed.


Serving: 1muffin | Calories: 259kcal | Carbohydrates: 52g | Protein: 6g | Fat: 8g | Saturated Fat: 1g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 2g | Trans Fat: 0.03g | Cholesterol: 42mg | Sodium: 172mg | Potassium: 221mg | Fiber: 3g | Sugar: 21g | Vitamin A: 154IU | Vitamin C: 16mg | Calcium: 146mg | Iron: 2mg
Have you tried this recipe?Mention @eileen.bakingsense or tag #bakingsense!

You might also like:

zucchini bread
Zucchini Bread
zucchini pie
Zucchini Pie
zucchini yeast bread
Zucchini Yeast Bread
Zucchini Biscuits
Zucchini Biscuits
sunflower crumb muffin on a plate
Sunflower Crumb Muffins
Recipe Rating

Stacey Bartlett

Monday 3rd of August 2020

Do you think you could make this in a loaf pan... Like a bread?

Eileen Gray

Monday 3rd of August 2020

Yes, this would probably work as a quick bread. Obviously you'll have to adjust the baking time.

Cara Hull

Saturday 19th of October 2019

Definitely just made these with no sugar (not on purpose) ... for sure adding the icing to see if that helps! They are just more savory now LOL

Eileen Gray

Sunday 20th of October 2019

Oh, well. Without sugar they'll not only be more savory, but also less tender. Hope the icing helps.

Jane Raskin

Sunday 8th of July 2018

in the Summer Squash Lemon Poppy Seed Muffin recipe, please clarify what type of sugar is called for. The list of ingredients says granulated sugar but the Instructions refer to brown sugar. Thank you


Monday 9th of July 2018

Hi Jane. Thanks for catching that. It should be granulated sugar.


Friday 29th of June 2018

Wow - these muffins look moist and fluffy! I've never heard anything about soaking poppy seeds before, but I'm definitely intrigued. Looking forward to trying the recipe!


Friday 29th of June 2018

Thanks! They are tasty!