The Best Grain-Free Zucchini Muffins—A Paleo Recipe to Kickoff the New Year

For me, the start of January is all about delicious and wholesome recipes that make meal prep feel effortless. As part of my gut-health journey, I’m currently eliminating grains and it’s made a really positive difference in how I feel. Although I’ve found cooking grain-free to be relatively simple and intuitive, grain-free baking definitely requires some experimentation. Through trial-and-error, I’m slowly honing in on my favorite recipes that use grain-free alternatives like almond flour, coconut flour, and cassava flour. And these grain-free zucchini muffins with chocolate chunks are my favorite baking experiment so far! If you’re on a grain-free or paleo diet or simply looking for a nutritious and tasty breakfast idea, you’re going to love these muffins.

These grain-free zucchini muffins make a satisfying breakfast (and a healthy lunchbox addition for my kids’ school lunches.) Read on for why you might consider cutting back on grains, what you need to make these deliciously satisfying muffins, and optional ingredient swaps to try.

grain free zucchini muffins

Why I Eliminated Grains From These Muffins

I’m working on a post that deep dives into why I’m currently following a grain-free diet (it’s essentially cured the gut health issues that have affected me for years!) While grains are certainly not “bad” and can even be a really healthy part of some people’s diets, there are a variety of reasons why someone may choose to eliminate or cut back on grains.

  1. Lower Carb Content: Traditional muffins typically contain wheat, which is high in carbohydrates. Our grain-free version cuts down on carbs, making it a great choice for those following a low-carb or ketogenic diet.
  2. Gluten-Free: Going grain-free means avoiding gluten, making these muffins suitable for individuals with gluten sensitivities or celiac disease.
  3. Nutrient-Rich Ingredients: Our recipe features nutrient-dense ingredients like seeds, nuts, zucchini, and coconut, providing essential vitamins, minerals, and healthy fats.
  4. Improve digestive health: Eliminating grains can reduce digestive discomfort and inflammation for some people (hand raised!)
  5. Enhance energy levels: A grain-free or paleo diet may help stabilize blood sugar levels, leading to sustained energy throughout the day.
  6. Support weight management: Lowering grain consumption often correlates with better weight control due to reduced carb intake.
  7. Reduce inflammation: Some find that avoiding grains can alleviate chronic inflammation and related health issues.

Now that you’re curious about giving grain-free baking a try, let’s dive into our Grain-Free Zucchini Muffin recipe.

grain free zucchini muffins

What You Need for Grain-Free Zucchini Muffins

  • eggs
  • whole milk (or non-dairy milk)
  • brown sugar (I used the natural sugar substitute Swerve to avoid raising blood sugar levels)
  • orange juice
  • melted butter (or melted coconut oil for a dairy-free option)
  • vanilla extract
  • kosher salt
  • unsweetened shredded coconut
  • sunflower seeds
  • almond flour
  • coconut flour
  • baking powder
  • zucchini
  • walnuts
  • dark chocolate chunks (you can use Hu chocolate for a paleo-friendly option)
grain free zucchini muffins

How to Make Grain-Free Zucchini Muffins

This is a simple recipe that takes about 20 minutes start-to-finish. First, you’re going to blend together the wet ingredients: eggs, milk, brown sugar or Swerve, orange juice, melted butter, and vanilla.

Then, you’re going to grind up your coconut and sunflower seeds in a blender or food-processor. These form a nutrient-packed “flour” and also add really delicious texture to these muffins.

Finally, you add all your dry ingredients to the mixer, blend it up, and then stir in the grated zucchini, walnuts and chocolate. Spoon them into muffin cups, add your toppings, and bake!

Optional Ingredients Swaps

Feel free to customize this recipe to your preferences and dietary needs. Here are some optional ingredient swaps that work well in this recipe:

  • Use your favorite nut milk in place of the whole milk for a dairy-free and paleo-friendly version.
  • Substitute brown sugar with a natural sugar substitute like Swerve for a lower sugar option. This is what I do, and I swear my kids have no clue that these are free of added sugars.
  • Choose your favorite nuts or seeds for added texture and flavor. Try adding toasted pecans instead of walnuts, omit the chocolate if you like, and you can use pumpkin seeds instead of the sunflower seeds.
grain free zucchini muffins

How to Store and Freeze These Muffins

I make a batch of these on the weekend, and then pop in the freezer so they’re ready for snacks and school lunches all week. To keep your Grain-Free Zucchini Muffins fresh and ready for a quick meal, follow these storage tips:

  • Store in an airtight container in the fridge for up to 4 days.
  • When reheating, warm them in the oven or halve and toast before serving for that perfect, crispy texture.
  • For longer storage, freeze the muffins in an airtight container for up to 2-3 months. Thaw them in the fridge or reheat from frozen. Here’s exactly how to freeze muffins for best results.

My Grain-Free Zucchini Muffins are not only delicious but also packed with wholesome nutrients for all-morning energy that won’t leave you crashing by 11am. Whether you’re following a paleo diet or simply looking for a grain-free treat, these muffins will satisfy. Read on for the recipe…


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These healthy grain-free zucchini muffins are a paleo-friendly breakfast, or an easy grab-and-go-snack.

  • 2 eggs
  • 1/4 cup whole milk (or your favorite non-dairy milk)
  • 1/4 cup brown sugar (or natural sugar substitute like Swerve)
  • 1/4 cup orange juice
  • 1/4 cup melted butter (or melted coconut oil for paleo or dairy-free)
  • 1 tablespoon vanilla extract
  • 1/2 teaspoon kosher salt
  • 1 cup unsweetened shredded coconut
  • 1 cup sunflower seeds (I use roasted and salted seeds)
  • 1 cup almond flour
  • 1/4 cup coconut flour
  • 2 tsp baking powder
  • 2 small zucchini, grated (about 3 cups)
  • 1/3 cup toasted walnuts
  • 1/3 cup dark chocolate chunks (use a brand like Hu for paleo)
  • For garnish: coconut flakes, chopped raw walnuts, sunflower seeds

  1. In the bowl of a stand mixer, beat together eggs, milk, brown sugar, orange juice, melted butter, and vanilla until fully combined.
  2. In a high-speed blender (or food processor), pulse the coconut and sunflower seeds until they’re a flour-like texture. You’ll know it’s ready when it starts to clump in the corners of the blender–don’t go past this because you don’t want them to release their oil. 
  3. Add to the ground coconut and seeds to the wet ingredients. Add both flours and baking powder, then use a fork to lightly toss the dry ingredients together.
  4. Turn the mixer on low speed and beat just until combined, scraping down the bowl halfway through. Add the zucchini, walnuts, and chocolate, and stir with a spatula until just combined. 
  5. Spoon into muffin cups and top with coconut flakes, walnuts, and seeds. Bake 35 minutes, until a toothpick inserted comes out clean. Remove from the oven and let sit in the muffin tin for about 5 minutes before transferring to a cooling rack to cool completely.
  6. Store in an airtight container in the fridge for up to 4 days. Warm in the oven or halve and toast before serving (preferably with a little melted butter!)


The ingredients in this recipe were inspired by the one from Whole Food Cooking Every Day, by Amy Chaplin. This is one of my favorite resources for gluten-free and grain-free cooking.

  • Prep Time: 20
  • Cook Time: 30
  • Category: breakfast

Keywords: breakfast, grain-free breakfast ideas, grain-free zucchini muffins