These Healthy Chocolate Muffins are naturally sweetened, have added butternut squash for an extra healthy punch of goodness, are gluten free, dairy-free and are so delicious! Plus, they are super easy to make and kid-approved!

chocolate butternut squash muffins in a bowl on a white table.

A good muffin recipe is my young daughter’s love language. Breakfast, lunch, dinner, snack, the middle of the night… girl loves her muffins and I love how much goodness I can shove into her favorite food. 

With school back in season, I have been dreaming up all the easy nut-free options that I can throw into her lunch box that are not only delicious and sure to be gobbled up, but that are also nutrient dense….which means veggies, protein and healthy fats.

Many of you know and love my nut butter based baked goods like…..

…but many of you have also said that you desperately need easy peasy nut-free options to feed to your kiddos! Which is why Healthy Chocolate Muffins (with butternut squash) happen to be nut-free.

Fun Fact: Did you know that when you combine sunflower seed butter (the base for this recipe) with baking soda, it turns GREEN when baked.

This is because sunflower seeds contain chlorophyll (or chlorogenic acid). This acid reacts with the baking powder/soda in a recipe when heated. And everything might look all fine and dandy straight from the oven, but once the baked good cools, it also turns green! 

A fun little thing to do for St. Patrick’s Day, but it often weirds people out to have an unexpectedly green baked good! Hence why I added cacao/cocoa powder to this recipe. It hides the strange green color and chocolate makes everything more appealing…for kids and adults.

And because I view every food offering as an opportunity to eat a veggie, butternut squash also made it into the mix!

a process shot of how to make chocolate muffins

Healthy benefits of butternut squash

It is almost fall, after all, and those beautiful butternut squashes are popping up everywhere!

Butternut squash is not only lovely to look at, but they are loaded with vitamin C,  vitamin E, thiamin, niacin, vitamin B-6, manganese and more potassium than a banana. With all that goodness, why wouldn’t I throw it into a sweet little muffin recipe that I know my girl will be going for first at lunch time?

Chocolate muffins cooling in muffin tin

Suggested adaptations when making Healthy Chocolate Muffins

  1. Not butternut squash? Pumpkin or sweet potato will work just fine, too! I find butternut squash, sweet potato and pumpkin to be very interchangeable in many recipes!
  2. Green doesn’t scare you? Leave the cacao/cocoa powder out! I personally love chocolate, but also know it is not everyone’s jam. If the chemical reaction between the sunflower seed butter and the baking soda resulting in a green muffin (that tastes just fine) doesn’t bother you, feel free to leave the chocolate out of this recipe all together!
  3. Chocolate chips are totally optional! Chocolate chips are a great way to adjust the sweetness/sugar level of these muffins to your personal tastes and needs. These muffins were sweet enough on their own for my family, so I just topped them with a few chocolate chips for fun and to make them more visually appealing. Feel free to omit them entirely for a lower sugar option or add as many as you like for a special treat that also has a punch of veggies!

Other butternut squash recipes you are going to love…..

Did you try this veggie-loaded muffin recipe and now you’re hungry for more? 

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chocolate butternut squash muffins on a white table with muffins in a bowl in the background
4.83 from 29 votes

Healthy Chocolate Muffins (with butternut squash)

Yield: 12 muffins
Prep Time: 5 minutes
Cook Time: 20 minutes
Cuisine: American
Course: Dessert
These healthy chocolate muffins are naturally sweetened, have added butternut squash for an extra healthy punch of goodness, are gluten free, dairy-free and are so fluffy and delicious! Plus, they are super easy to make and kid-approved!



  • Preheat your oven to 350F and line a 12-hole muffin tin.
  • Combine all ingredients (except chocolate chips, if using) in a large bowl. Mix until all ingredients are incorporated.
  • Add chocolate chips (if using) and stir to mix them in.
  • Using a spoon or small measuring cup, portion out the batter between the 12 lined muffin tin holes.  Top with more chocolate chips, if desired.
  • Bake for 20 minutes or until a toothpick inserted in the middle of the muffin comes out clean.
  • Let cool for 20 minutes and enjoy.
  • Let cool completely before storing in an air-tight container in your fridge or freezer.


*Chocolate chips often contain dairy, so if dairy-free is important to you, be sure to pick a dairy-free brand.
Serving: 1muffin, Calories: 181kcal, Carbohydrates: 17g, Protein: 6g, Fat: 11g, Saturated Fat: 3g, Cholesterol: 54mg, Sodium: 80mg, Potassium: 114mg, Fiber: 1g, Sugar: 9g, Vitamin A: 1032IU, Vitamin C: 2mg, Calcium: 52mg, Iron: 1mg