Kalyn's Kitchen

Whole Wheat Zucchini Muffins with Green Chiles and Cheese

Whole Wheat Zucchini Muffins with Chiles and Cheese took quite a few tries to perfect the recipe, but the final version of these muffins are loaded with savory flavor! 

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Whole Wheat Zucchini Muffins with Green Chiles and Cheese on cutting board

If you have a garden or you get zucchini in your CSA box, by now you may have made grilled zucchini, stuffed zucchini, cheesy zucchini, zucchini salad, or even left some zucchini on your neighbor’s porch!  When I’m overloaded with zucchini and I’ve tried all the recipes I can think of, I start making zucchini bread.  I’ve made quite a few variations of sweet zucchini breads and muffins for the blog, but this time I wanted a savory zucchini muffin.

I wanted a muffin that included cheese and a fair amount of zucchini, and it took me seven tries to get a recipe I was satisfied with, but the happy result was these Whole Wheat Zucchini Muffins with Green Chiles and Cheese. I’m glad I persisted until I had a winner because I loved the muffins warm with a bit of butter!

Process shots collage for Whole Wheat Zucchini Muffins with Green Chiles and Cheese

How to Make Whole Wheat Zucchini Muffins with Green Chiles and Cheese:

(Scroll down for complete recipe with nutritional information.)

  1. I used a combination of grated yellow squash and zucchini, but use whichever you have a surplus of. I grated it with my food processor, but a large hand grater will work too.
  2. My first few tries were way too wet, so some good bakers gave me the tip of putting the zucchini inside a dish towel and squeezing out all the liquid. I highly recommend doing that!  You’ll be amazed at how much water comes out.
  3. Drain a small can of whole green chiles, then stack them up and chop into very small pieces. Then take a paper towel and cover the diced chiles, pressing down so the towel absorbs even more of the juice. They should look fairly dry like this when you put them into the bowl. (When I used green chiles that come already diced, they were too wet.)
  4. In a medium-sized bowl, combine the grated zucchini or squash, diced green chiles, grated cheese, and finely grated Parmesan. Then beat together the buttermilk and eggs and mix it into these wet ingredients.
  5. In a small bowl, combine the White Whole Wheat Flour (affiliate link), sweetener, sea salt, baking soda, and baking powder.
  6. Add the dry ingredients to the wet ingredients and mix until the flour is all incorporated into the batter. (The dough will be stiff and hard to stir.)
  7. Spray muffin tins or silicone baking cups and fill them full but not overflowing.  (I had a tiny bit of dough left, which I baked in a mini-loaf pan.)
  8. Bake the muffins at 350F/180C for about 50 minutes, or until the outside is nicely browned and muffins are cooked through. (They will be moist inside when they’re still hot.  I was surprised they took so long to bake until I realized how many wet ingredients there were.)
  9. Let muffins cool about 15 minutes before eating them.  They keep well in the fridge and reheat well in the microwave (only about 30 seconds.)

Savory Whole Wheat Zucchini Muffins with Green Chiles and Cheese found on KalynsKitchen.com

More Tasty Ideas for Zucchini:

The BEST Slow Cooker Zucchini Recipes from Food Bloggers ~ Slow Cooker or Pressure Cooker
Low-Carb and Flourless Zucchini Muffins with Pecans ~ Kalyn’s Kitchen
Cinnamon Zucchini Muffins ~ Barbara Bakes
Low-Sugar and Whole Wheat Zucchini Bread with Blueberries and Pecans ~ Kalyn’s Kitchen

Whole Wheat Zucchini Muffins with Green Chiles and Cheese on cutting board

Whole Wheat Zucchini Muffins with Green Chiles and Cheese

Yield 15 small muffins
Prep Time 30 minutes
Cook Time 50 minutes
Total Time 1 hour 20 minutes

These Whole Wheat Zucchini Muffins with Chiles and Cheese are loaded with amazing savory flavors.


Wet Ingredients:

  • 1 1/2 cups grated zucchini or yellow squash, squeezed in a dish towel until no more liquid comes out
  • one 4 oz. can whole green chiles, drained well and finely diced
  • 3/4 cup grated Mexican Blend cheese
  • 1/4 cup very finely grated Parmesan (the kind in a can is fine)
  • 1/4 cup buttermilk
  • 2 eggs

Dry Ingredients:

  • 1 1/2 cups white whole wheat flour
  • 1/4 cup Granulated Monkfruit Sweetener
  • 1 tsp. sea salt
  • 1 tsp. baking soda
  • 1 tsp. baking powder


  1. Preheat oven or toaster oven to 350F/180C.
  2. Spray muffin pan or silicone muffin cups with non-stick spray or oil.
  3. Grate zucchini or squash, using a food processor or the large side of a hand grater.
  4. Put grated squash into a dish towel and squeeze until no more water comes out.
  5. Measure the squash and put into a medium-sized bowl.
  6. Drain the whole green chiles, and pick off any seeds (unless you want it extra spicy.)
  7. Stack up the chiles on a cutting board and dice them into small pieces, then place a paper towel over the diced chiles and press down to absorb any extra water.  (You may need to do this with a couple of towels.)
  8. Add chiles and both types of cheese to the bowl with the squash.
  9. Beat together the eggs and buttermilk and then mix into the wet ingredients.
  10. In a smaller bowl, stir together the white whole wheat flour, sweetener, sea salt, baking soda, and baking powder.
  11. Add the dry ingredients to the wet ingredients, stirring together until all the flour is incorporated. (The batter will be stiff and hard to stir.)
  12. Fill muffin cups so they are full but not overflowing. (If you only have a small muffin pan with 12 cups, bake the extra in a small loaf pan.)
  13. Bake muffins about 50 minutes, or until they are nicely browned on the outside and cooked through. (I started checking them at 40 minutes, but I baked mine the full 50 minutes.)
  14. Muffins will have a slightly crisp crust and be somewhat moist inside.
  15. Let muffins cool about 15 minutes before eating.
  16. These muffins kept well in the fridge and were easily reheated (in a microwave for about 30 seconds.)
  17. I liked them hot, with a bit of butter.


You can make about 15 small zucchini muffins or 12 muffins and a small mini-loaf of zucchini bread. Or if you have larger muffin cups, this recipe will be perfect to make 12 muffins. I'm a fan of Monkfruit Sweetener (affiliate link), but use any sweetener of your choice.

Recipe created by Kalyn after many tries and a lot of consulting zucchini bread recipes on other blogs.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 91Total Fat: 3gSaturated Fat: 2gTrans Fat: 0gUnsaturated Fat: 1gCholesterol: 32mgSodium: 339mgCarbohydrates: 12gFiber: 2gSugar: 2gProtein: 5g

Nutrition information is automatically calculated by the Recipe Plug-In I am using. I am not a nutritionist and cannot guarantee 100% accuracy, since many variables affect those calculations.

If you make this recipe I'd love to hear how it turns out. Leave a star rating or share on social media with the hashtag #KALYNSKITCHEN, thanks!

Low-Carb Diet / Low-Glycemic Diet / South Beach Diet Suggestions:
Using white whole wheat flour and mostly low-fat cheese plus a generous amount of zucchini makes these Savory Whole Wheat Zucchini Muffins with Chiles and Cheese a good choice for phase 2 or 3 of the South Beach Diet and they’re suitable for most low-glycemic eating plans. Muffins with flour are too high in carbs for a low-carb diet.

Find More Recipes Like This One:
Use Bread Recipes to find more recipes like this one! Use the Diet Type Index to find recipes suitable for a specific eating plan. You can also Follow Kalyn’s Kitchen on Pinterest to see all the good recipes I’m sharing there.

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    28 Comments on “Whole Wheat Zucchini Muffins with Green Chiles and Cheese”

  1. Pingback: 25 Homemade Mother's Day Brunches | Homemade Recipes

  2. So glad you enjoyed the muffins!

  3. I made these muffins along with some butternut squash chili, and they went together perfectly! I love the slight hint of spiciness. Thanks for the recipe 🙂

  4. Kristie, so glad you enjoyed them. I tried the recipe several times and couldn't figure out why mine were taking so long to bake (unless it's because I have an enormous oven.)

  5. Thank you for the wonderful recipe! I tried these tonight and they were wonderful. I took them out at 30 minutes and they looked just like yours, so our ovens must cook a little differently. They would be perfect with soup. Thanks again!

  6. I do think this is a completely different take on traditional zucchini bread.

    Deborah, hope you will enjoy the muffins!

  7. My mother in law just brought over a ton of zucchini – I think these will be gracing our dinner table this week!

  8. I'm a huge fan of my mother's zucchini bread, but this is taking it to a whole new level! Looks amazing!