Flourless Chocolate Muffins (with butternut squash)
These gluten-free chocolate muffins are totally flourless, naturally sweetened with maple syrup or honey, have added butternut squash (or pumpkin!) puree for a boost of goodness are dairy-free easily nut-free. Mixed up in one bowl, they are not only super easy to make but chocolatey and kid-approved!

Just trust me, the orange veggies just make these chocolate muffins better….
A good muffin recipe is my young daughter’s love language. Breakfast, lunch, dinner, snack, the middle of the night…..my kid loves a muffin and I love how much goodness I can shove into that beloved, sure-to-be-eaten food.
With school back in season, I have been dreaming up all the easy nut-free options that I can throw into school lunch boxed that are not only delicious and sure to be gobbled up, but that are also nutrient dense. My daughter’s favorite muffins is a toss up between my flourless sweet potato peanut butter muffins and my veggie-loaded chocolate muffins. So, I thought…why not take the best bits of each a make a newer, school-lunch-box friendly muffin recipe. And, yeah, thats what brought these butternut squash loaded gluten free chocolate muffins into our lives.
To make these nut-free, I used sunflower seed butter, which behaves a lot like peanut butter or almond butter. I love sweet potato in a muffin, but I don’t always plan ahead enough to bake one….but always have a can of butternut squash puree or pumpkin puree on hand, so these are super easy to make with no forethought required. One bowl. Dairy-free when you use dairy-free chocolate chips. Delightfully and shockingly spongy despite there not be a crumb of flour in them. Just so good in so many ways. Oh and….
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 cocoa powder to this recipe. It hides the strange green color and chocolate makes everything more appealing…for kids and adults.
Let’s make these muffins together. Just you and me….

Tips for making these gluten free muffins from my kitchen to your’s
- 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!
- Green doesn’t scare you? Leave the 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!
- 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!


Flourless Chocolate Muffins (with butternut squash)
Ingredients
- ¼ cup maple syrup or honey
- 3 large eggs
- ⅓ cup cocoa powder
- ¾ cup no-sugar added sunflower seed butter, if nut-free isn't important, you can sub natural smooth peanut butter or almond butter
- ¾ cup butternut squash puree, or pumpkin puree
- ½ teaspoon ground cinnamon
- ½ teaspoon baking soda
- 1 teaspoon apple cider vinegar, or white vinegar
- 1 teaspoon vanilla extract
- ½ cup chocolate chips*, or to taste and optional
Instructions
- Preheat your oven to 350℉ 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.


Hi! Love this recipe, two questions about substitutions, can I substitute the apple cider vinegar for anything else? And lastly can I use normal butter or margarine as I don’t like nut butters & can’t find sunflower seed butter anywhere! I know technically you can google substitutions but you never know with the flavour and other ingredients etc. Thanks :)))
Hi Elise! So glad you love this one! The apple cider vinegar offers an acid to the recipe and helps to give the muffins lift as well as balancing out flavors. It can be replaced with white vinegar or even lemon juice. As for butter and margarine, unfortunately they don’t behave the same way as sunflower seed butter or nut butter in cooking and can’t be used place of them in these. I wish I had another sub to suggest, but since the nut/seed butter is the base of these muffins vs flour, there really is no alternative that will work.
Hi! Love this recipe, two questions about substitutions, can I substitute the apple cider vinegar for anything else? And lastly can I use normal butter or margarine as I don’t like nut butters & can’t find sunflower seed butter anywhere! I know technically you can google substitutions but you never know with the flavour and other ingredients etc. Thanks :)))