These whole wheat summer squash chocolate chip muffins are so moist and tender! They combine zucchini and yellow squash with a hint of orange, cardamom, and mini chocolate chips! 

Whole wheat summer squash chocolate chip muffins in baking pan

I feel like a lot has changed for me in the last month. My real world job, where I work as a private chef, has been non-stop busy since I took it over a year ago. I am head over heels in love with the job. But because of the craziness with the number of hours I work, frequent travel, inconsistent schedule, and never ending things to do, I will admit, I haven’t taken very good care of myself this last year.

But over the last month I have been working really hard on changing that! I have been eating properly, exercising regularly, and finding so much joy and peace in spending time outside. I am very spoiled to have the lake literally right outside my doorstep and I have been taking so much advantage of it. It makes me infinitely happy to be by the water and I am trying to soak in every second of summer before the winter hits!

Last year was about finding happiness in the best job and this year is about taking care of myself and finding happiness in that! Summer feels like perfect time to start that, right?!

Fresh green and yellow squash

I wanted to bake something that celebrated the feeling of summer that I’m experiencing right now. Something a little decadent but not too crazy. I found these beautiful summer squash at my farmer’s market and decided that I wanted to highlight them. Muffins seemed like the perfect vessel so I could share them with some friends easily!

Because this is such a moist muffin, it stands up well to whole wheat flour. Sometimes recipes that use all whole wheat flour as the structure can be tough and have a bit of a coarse grain. These do not at all! They are perfectly tender and moist because of the squash and the wheat flour gives a good heartiness that makes these taste like they are right out of a bakery.

Whole wheat summer squash chocolate chip muffin with a bite taken out

I wanted to give a little brightness to these, so I added some orange juice and zest and also threw in a little cardamom. The cardamom is absolutely optional, because I know everyone doesn’t have it lying around their pantry, but if you do have it don’t skip it! It gives such a beautiful flavor to these muffins. (Side note: I totally believe everyone should have cardamom lying around their pantry. So if you don’t, seriously consider.)

Here is how to make them…

Green and yellow squash grated and being drained

Start by shredding 2 cups each of zucchini and yellow squash. No need to peel them. The color makes these muffins really beautiful!

Paper towels on top of the squash to remove the moisture

Take a few layers of paper towels and press out as much moisture from the squash as possible. This will prevent there being too much liquid in your muffins. They could fall apart if you skip this step.

Wet ingredients being whisked together

Start by whisking together your wet ingredients. If you remember from my post about The Muffin Mixing Method, sugar is almost always included in with the wet ingredients when making muffins and quick breads.

Fresh squash added to wet ingredients

Fold in your zucchini and squash and then we are on to the dry ingredients!

Dry ingredients added to wet ingredients

Add all of your dry ingredients into the bowl and make sure you are using a spoon and not a whisk at this point. We want to keep the muffins very tender, so stir just until the dry ingredients are almost all incorporated.
Chocolate chips added to muffin batter

When there is just a little flour left to be stirred in, add the chips and finish stirring. Making sure you don’t stir too much is key to keeping your muffins very light and tender.
Muffin batter poured into parchment cups in baking pan

Fill your muffin tins with your batter. This recipe will make 12 very large muffins, or you can make 16 or 24 smaller ones.

Whole wheat summer squash chocolate chip muffins fresh out of the oven

Even after sharing with friends, I still had a few of these leftover so I wrapped a few in plastic wrap and thew in the in the freezer. They re-heat beautifully! I have tried one in the microwave on 30% heat and also have tried it in the oven @ 300F. Works great as a quick treat or breakfast!

Whole wheat summer squash chocolate chip muffins in baking pan
Yield: 12 Muffins

Whole Wheat Summer Squash Chocolate Chip Muffins

Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes

These Whole Wheat Summer Squash Chocolate Chip Muffins are so moist and tender! They combine zucchini and yellow squash with a hint of orange, cardamom, and mini chocolate chips.


  • 2 cups (about 8 oz, 225 gr) shredded yellow squash
  • 2 cups (about 8 oz, 225 gr) shredded zucchini
  • 3/4 cup (5,25 oz, 147 gr) granulated sugar
  • 3/4 cup (6 oz, 168 gr) brown sugar, lightly packed
  • 4 large eggs, room temperature
  • 3/4 cup (6 oz, 168 gr) vegetable oil
  • 3 TBSP (1.5 oz, 42 gr) orange juice
  • 2 tsp orange zest
  • 1 tsp vanilla extract
  • 2 3/4 cup (11.7 oz, 327 gr) whole wheat flour
  • 3/4 tsp kosher salt
  • 1 TBSP baking powder
  • 1/2 tsp baking soda
  • 1 tsp cinnamon
  • 1/4 tsp cardamom (optional)
  • 1 cup (6 oz, 168 gr) mini chocolate chips


  1. Preheat the oven to 350F. Line a regular 12 cup muffin tin with liners or spray well with non-stick spray.
  2. Shred the squash and zucchini and place in between several layers of paper towels. Press out as much moisture from the veg as you can. Set aside.
  3. In a large bowl combine the granulated sugar, brown sugar, eggs, vegetable oil, orange juice, orange zest, and vanilla extract. Whisk together until well combined. Stir in the shredded zucchini & squash.
  4. Add the wheat flour, salt, baking powder, baking soda, cinnamon, and cardamom (if using) to the bowl. Use a spoon instead of a whisk, and stir the dry ingredients into the wet ingredients until almost combined. Add the chocolate chips and continue stirring just until all of the ingredients are incorporated. Do not stir more than needed. This will keep your muffins light and tender.
  5. Bake at 350F for 20-25 minutes, until a toothpick inserted in the center comes out with moist crumb.
  6. Cool on a wire rack. Best eaten the day of, or the muffins can be cooled completely and wrapped in plastic wrapped and stored in the freezer for up to 6 months.

Nutrition Information:

Amount Per Serving: Calories: 0