Easy Almond Flour Chocolate Zucchini Muffins (Gluten & Dairy-Free)

In 30 minutes or less, make these delicious and easy Almond Flour Chocolate Zucchini Muffins. With 8 simple ingredients, you’ll have muffins ready to enjoy with breakfast, as a midday snack, or even for dessert!

Muffins are a convenient and nutritious treat to have on hand in your kitchen. If you’re in a hurry, you can enjoy them cold or at room temperature. They are easy to warm up in a microwave or toaster oven days after you make them. Try combining them with fruit or a warm beverage for a delicious, decadent treat.

Why Use Almond Flour?

Some people with IBD may not tolerate gluten found in wheat-based foods. For some, it can trigger flare ups or other uncomfortable symptoms in the gut. Others may be following a gluten-free IBD therapeutic diet to help with IBD symptoms.

With these Gluten-Free Chocolate Zucchini Muffins, almond flour makes a great alternative to wheat flour. Made from ground almonds, almond flour contains protein, Vitamin E, and healthy dietary fats. It also adds natural sweetness to your muffin!

Making your own muffins can help avoid hidden sources of gluten or other food additives found in many store-bought products.

Do You Peel Zucchini Before Shredding for Zucchini Muffins?

In this recipe, yes, but it’s really up to you! Most of the vegetable flavor and fiber in zucchinis lives in the skin. You can still get key nutrients like potassium in your chocolate muffin without the peels, without the zucchini flavor and without extra fiber during a flare up.

4 Reasons to Keep Zucchini Skin on for Baking

  1. Flavor Impact: Zucchini skin has a slightly more noticeable zucchini flavor compared to its flesh. The inside has a mild and neutral taste. By peeling it, that ‘zucchini’ taste is less noticeable in your muffins. This can be especially helpful if you’re making muffins for anyone who might be a bit wary of veggies in their dessert!
  2. Texture Variation: Keeping the skin of the zucchini will give your muffins a more noticeable texture, similar to carrot cake. Without it, your muffins will have a more even, soft texture.
  3. Nutritional Level: Keep in mind that zucchini skin is rich in nutrients and insoluble fiber. Peeling off the skin can be helpful during an IBD flare to reduce the amount of insoluble fiber. But during times when you’re feeling better, you can absolutely keep the skin on this recipe to get even more nutrients.
  4. Visual Appeal: The green flecks of zucchini skin can add a nice visual contrast to the muffins, hinting at their hidden vegetable content. Peeling the zucchini helps to achieve a more chocolate-dominant look.

Nutritional Benefits of Chocolate Zucchini Muffins at a Glance

These zucchini chocolate muffins make a great breakfast or snack and contain IBD-friendly ingredients. Just one muffin is a good source of magnesium (16% DV), one of the top 10 nutrients that I find my IBD clients are often deficient in.

Almond Flour Benefits

Almond flour contains protein, Vitamin E and healthy dietary fats. Vitamin E is an important antioxidant that helps with inflammation in the body. It’s also a good source of manganese and magnesium. Try using almond flour as a gluten-free alternative in your IBD-friendly baking.

Zucchini Benefits

Zucchini is a type of summer squash rich in minerals such as potassium and manganese. It’s a great source of Vitamin C and B6 and insoluble fiber. These easy cocoa muffins with zucchini bring important nutrients for a healthy IBD diet!

Olive Oil Benefits

Olive oil is a great replacement for butter, often found in muffin recipes. It is high in unsaturated fats called monounsaturated fats. Its natural polyphenols are great for anti-inflammation and disease-prevention, and may help regulate intestinal muscle contractions. It contains good amounts of Vitamin E and Vitamin K.

Cocoa Powder Benefits

Cocoa powder is created by removing the fat from cocoa. It is known for being rich in polyphenols. A specific kind called flavonols, are known for their antioxidant and anti-inflammatory properties. Studies have shown these polyphenols function as prebiotics to support the growth of healthy bacteria in the gut.

Maple Syrup Benefits

Maple syrup adds just enough sweetness and moisture! It skips the refined sugar typically found in muffin recipes. It can be a source of some zinc, manganese and antioxidants. However, it should still be consumed in moderation given its sugar content.

Chocolate Zucchini Muffins can Help Maintain your Diet Plan

These easy zucchini muffins meet a lot of different diet needs and avoid common triggers for IBD:

  • Dairy Free
  • Gluten Free
  • Grain Free
  • Corn Free
  • Soy Free
  • Beef Free
  • Chicken Free
  • Legume Free
  • Nightshade Free
  • Pork Free
  • Seafood Free
  • Vegetarian
  • Pescatarian
  • Kosher
  • Paleo

Tips for Moist Cocoa Zucchini Muffins

  • Don’t overmix once you add all the ingredients together.
  • Try not to overbake the muffins.

How to Make Chocolate Zucchini Muffins

Start by preheating the oven and prepping a 12-cup muffin tray. Mix the dry ingredients in a large bowl. Keep the grated zucchini on the side. Mix the wet ingredients separately in a medium bowl. Add the wet ingredients to the dry ingredients and fold until just combined. Do not overmix. Add the zucchini to the mix and stir gently. Spoon the muffin batter evenly in the muffin tray and bake!

A dark countertop displays a muffin tray filled with glossy, deep-red mixture in each cup. Adjacent to the tray is a fresh, green zucchini with a striped cloth beneath. A small sprig of herbs lies at the upper right corner of the image.

Easy Almond Flour Chocolate Zucchini Muffins

Renata Cauchon-Robles and Danielle Gaffen, MS, RDN, LD
Total Time 30 minutes
Course Breakfast, Dessert, Snack
Servings 12 Servings
Calories 188 kcal


  • 1 Muffin Tray
  • 12 Muffin liners or use a silicone muffin tray


  • 2 cups Almond Flour
  • 1/4 cup Cocoa Powder
  • 1/4 tsp Sea Salt
  • 1/4 tsp Baking Soda
  • 1/4 cup Extra Virgin Olive Oil
  • 1/4 cup Maple Syrup
  • 3 large Eggs
  • 1 medium Zucchini peeled, grated


  • Preheat the oven to 350ºF (177ºC) and line a muffin tray with liners. Brush each liner with a small amount of coconut oil or use a silicone muffin tray.
  • In a large mixing bowl, combine the almond flour, cocoa powder, sea salt, and baking soda. Mix well.
  • In a medium-sized bowl, whisk together the oil, maple syrup, and eggs. Add the wet ingredients to the dry. Mix until combined then stir in the zucchini.
  • Spoon the muffin batter into the prepared muffin tray, so it's evenly divided then bake for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Let cool completely before eating, to prevent the muffins from sticking to the liners.


Serving Size
One serving is equal to one muffin.
One medium zucchini is equal to about 2 cups of grated zucchini.
Store in the fridge for 5 days or in the freezer for a few months.


Serving: 1ServingCalories: 188kcalCarbohydrates: 10gProtein: 6gFat: 15gSaturated Fat: 2gPolyunsaturated Fat: 1gMonounsaturated Fat: 4gCholesterol: 47mgSodium: 96mgPotassium: 101mgFiber: 3gSugar: 5gVitamin A: 100IUVitamin C: 3mgCalcium: 59mgIron: 1mg
Keyword corn-free, dairy-free, gluten-free, grain-free, kosher, legume-free, muffin, Paleo, soy-free, vegetarian

Almond flour zucchini muffins aren’t the only food that can help you! Learn to eat for IBD remission with an evidence-based 12-week course led by a Registered Dietitian Nutritionist. 


About the Author

Picture of Danielle Gaffen, MS, RDN, LD

Danielle Gaffen, MS, RDN, LD

Understanding the link between nutrition and gut disease prompted me to obtain my master’s degree in Nutritional Sciences at San Diego State University and become an IBD Registered Dietitian Nutritionist. Now I work with people who have Crohn’s and colitis who are struggling with confusion around what to eat. My favorite part is helping them to build confidence to eat without fear while managing their symptoms.

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