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!
A good muffin recipe is my young daughter’s love language. Breakfast, lunch, dinner, snack, the middle of the night…..my 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…..
- Peanut Butter Pumpkin Bread
- Sweet Potato Peanut Butter Muffins
- Almond Butter Blueberry Zucchini Muffins
- Flourless Chocolate Protein Donuts (with hidden veggies!)
…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!
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?
Suggested adaptations when making Healthy Chocolate Muffins
- 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 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!
- 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…..
- How to cook butternut squash (6 ways!)
- Healthy Egg-Free Brownies (with butternut squash)
- Slow Cooker Chicken & Butternut Squash Stew
- Butternut Squash Banana Blender Muffins
- Slow Cooker + Instant Pot Butternut Squash Chicken Curry
- Instant Pot Black Bean & Butternut Squash Soup
- One-Pot Cheesy Butternut Squash Pasta
- Mini Whole Wheat Blueberry Muffins (with butternut squash)
Did you try this veggie-loaded muffin recipe and now you’re hungry for more?
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Healthy Chocolate Muffins (with butternut squash)
Ingredients
- 1/4 cup maple syrup or honey
- 3 large eggs
- 1/3 cup cacao powder or cocoa powder
- 3/4 cup no-sugar added sunflower seed butter if nut-free isn't important, you can sub natural smooth peanut butter or almond butter
- 3/4 cup butternut squash puree
- 1/2 tsp ground cinnamon
- 1/2 tsp baking soda
- 1 tsp apple cider vinegar
- 1 tsp pure vanilla extract
- 1/2 cup chocolate chips* or to taste and optional
Instructions
- 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.
Notes
Nutrition
The nutritional information is provided as an estimate only and may vary based on the product type, servings and other factors. If you are following a diet, please consult with a professional nutritionist or your doctor. Stay healthy!
Comments
Could natural peanut butter be substituted for the sunflower butter if I’m not worried about being nut free? Nothing against sunflower butter, but if I can sub then I have all needed ingredients on hand! 🙂
Never used butternut squash…so how do you make a puree?
You can buy it at the store or just roast a butternut squash and puree up the flesh in the blender!
These are healthy and yummy! I didn’t have any buttenut squash but I had a cooked sweet potato and a half of a banana and I mashed them together. They came out really good!
Such a great sub! yum!
We have to avoid eggs. What would be a good substitute for the 3 eggs? Flax eggs?
I’ve tried this kind of recipe with various egg replacements but I haven’t had success with any yet.
Such a brilliant idea to use butternut squash in muffins! I love all the amazing ways you hide veggies in desserts.
The more veggies, the better in my book! 😉
So fun! My girls have been asking for something with chocolate the last couple weeks – I’ll have to indulge them with these!
I hope they enjoy!
Such an awesome way to use butternut squash! I love the shiny crackly tops on these muffins – so yummy!
Thank you!
I love butternut squash but have never used it in muffins. YUM! Your muffins are beautiful!!
Thank you!
I love when all the butternut comes out of my garden…and what a beautiful way to use some puree!! These looks so decadent!
Thank you!
Love how simple and delicious this recipe is. How wonderful!
I am such a sucker for a recipe with some hidden veggies in it. The texture in these looks outta this world. Totally trying these as soon as I can!
These look like gorgeous muffins, perfect for nut free schools! I have to say I’d love to dunk my finger in the raw batter as it looks amazing! xxD
Do you think these could be made with nut butter instead? I’d rather not have to buy sunflower butter since we don’t have to worry about being nut free! Can’t wait to try these.
Yes! I make it with creamy almond butter often! Peanut butter would also work. Whichever you prefer!
I’ve made them with nut butter everytime works perfectly
I followed the instructions and combined all of the ingredients in a large bowl but I ended up with a super duper lumpy batter. The lumps were actually the cacao powder that just wouldn’t breakdown with the hand mixer or with a spoon. What do you think went wrong?
I have these in the oven now and used some leftover pumpkin. Using duck eggs since chicken eggs and I don’t get along. Batter tastes fab! Can’t wait for them to be ready.
I have literally made these 10 times in the last month I love them and so does my fiancé!
Love this!! I have a baby and 4 year old who doesn’t like chocolate (weird, I know) so I left out the cocoa and subbed blueberries. I made 8 of them that way and then added cocoa powder to four of them for myself!!! They smell AMAZING and the texture is super awesome from the looks of it. Thank you for another amazing recipe!!!!
Yay! I’m so glad it was a hit!
These are so yummy! My family was hooked on Eggo waffles in the morning (we all have to be out of the house by 7:20 AM every morning, so convenience is key!), but I was dissatisfied with the empty carbs they were eating daily. Now I make a batch of these on Sundays and I feel like everyone is getting a much healthier start to their day!
I LOVE this! So awesome!
Could you use almond butter in this? Also, don’t muffins usually have flour? Does the cocoa powder substitute for that?
We need to be nut and seed free. Any non seed and nut butter substitutions you could suggest? Thank you!
Oh that is a tricky one. I honestly can’t think of one that would work with this recipe. However, you might be able to add cocoa powder to this recipe and sub the sweet potato for butternut squash. I haven’t tried it, but it might work.
https://thenaturalnurturer.com/2016/11/17/grain-free-sweet-potato-muffins/
I don’t think I was clear-sorry! We are good with all vegetables- just can’t use but or sunflower seed butters. Just wondering if there was a healthy substitute for the sunflower butter besides almond butter. Thank you for the great recipes!
Not only do these taste amazing, they look as pretty as they do in the pictures! Definitely not a muffin that kids would detect a veggie in! I used puréed pumpkin simply because I’m lazy 🤗. Will make again!
Love it! I switch out the veggie in these as well!
These are out-of-this world good! My daughter asked to have them for her birthday cupcakes
Would this recipe work without the maple syrup? Or does it need added sweetness?
Thank you
I know some people make it without and like it, but I think you have to be okay with it not really being sweet. If you are used to or prefer a sweet muffin, I would keep it in or use another sweetener.
One of my kids’ (and husband’s) all time favorite recipes! And they are so easy to make!
These are delicious! I’ve made this recipe probably 10 times now. I double it so I can freeze some to have on hand for my chocolate sweet tooth. I typically use pumpkin in place of butternut squash because I have canned pumpkin on hand.
I LOVE freezing these!
I used peanut butter and added about 1 1/2 cups of grated carrots to the recipe. My food processor is broken so the way I grated the carrots made the texture a little funky, but otherwise I think it would work as a yummy addition to the recipe! Thanks for this delicious recipe!
The batter without eggs are delicious. I was wondering if it would cook well without the eggs?
I used pumpkin puree and flax eggs. They can out well. But the natural sweetness was gone when I added the flax eggs. Still, super yummy. My kids enjoy them as snacks.
I haven’t had a lot of success making these or nut butter based baked goods without eggs or with flax eggs, but I am so glad you did! Did they hold together okay?
I have an acorn squash that I have been trying to use up. Do you think these would work with acorn squash puree instead of butternut squash? Thank you! So excited to try.
I haven’t tried but I would think so! Just make sure to drain off any extra liquid, as homemade purees tend to be a bit wetter than canned!
Is it possible to try it with regular butter (can’t get the nut seed butter due to lockdown!). Can’t use any nut based butters either.
Unfortunately no. Nut butter and dairy butter are very different. But this recipe might be a better fit for you
https://thenaturalnurturer.com/egg-free-chocolate-butternut-squash-muffins/
I don’t have ACV on hand. What would be a good substitute? Or could I just go without? I’m not sure what purpose it serves in the recipe or I’d try to think of a sub on my own!
The ACV is the acid in the recipe that activates the baking soda. You can use lemon juice too or I often use this sub for baking soda in recipes
1 teaspoon baking soda = 3 teaspoons baking powder + omit any added salt
can i use stevia sugar
I haven’t tried it but I bet it would work!
Are the nutrition facts for all 12 or just 1?
1 muffins
Any substitute for apple cider vinegar?
Lemon juice would work!
Like!! I blog frequently and I really thank you for your content. The article has truly peaked my interest.
most excellent
I’m afraid I didn’t love these muffins, although was impressed that the texture was good considering they contain no flour or oats. I love the Oatmeal Green Smoothie Muffins (have a batch in the freezer right now), so that made me think these might surprise me, but the flavor combo with these ratios of peanut butter, pumpkin and chocolate didn’t work for me. Am wondering about leaving out the chocolate, but maybe instead need to try the butternut squash banana blender muffins and the paleo zucchini blueberry muffins, and get almond butter for the latter so I’m not subbing peanut butter. I love your interesting healthy combos of ingredients for muffins and I’m sure several of the other recipes will be more to my liking.
I’m glad you tried it! Not every recipe is going to be for everyone and I totally get that! I’m so glad you enjoy other TNN recipes!
I have tried soo many healthy brownie/choc muffin recipes in the quest for a guilt-free sweet treat and this recipe tops all of them! I initially made these to trick my toddler into eating squash but then I ended up eating up half the batch with some cool whip smeared on top. They are addictive!! I made mini muffins using natural peanut butter (made about 45, cook for 12 min instead) and they were perfect. Thank you!!
I am so glad they were a success with the whole family! And, yum, whipped cream “frosting” is the best!
I love love love your other chocolate muffins and your green pancakes but my family and I sadly didn’t like these muffins at all which is weird because I love chocolate and peanut butter. I used honey and peanut butter and they just tasted like bitter peanut butter. There was no sweetness at all despite the addition of chocolate chips.
Hi Chase! So sorry this recipe didn’t work out for you, though I am glad other TNN recipes are enjoyed by your crew! These muffins are certainly milder in sweetness, which is not everyone’s cup of tea. Did you reduce the sweetener or chocolate chips in the recipe? I’m wondering if 1/4 of cup cocoa powder might be more to your liking if you ever give this recipe another go! Thanks for the feedback, just the same!
SO GOOD! I have been making muffins for a few years now. They are a staple in our house! I always use pumpkin puree, as I have it in the house. I tried using sun butter for the first time this week (instead of peanut butter) and they were even better! Thank you for this recipe!
I am so glad, Jen! Thank you for taking the time to share all of that!
These were SO GOOD!!!! My 15 month old and 3 year old gobbled them up. Thank you!!!!
I am SO happy to hear that, Amanda!
My kids are muffin monsters, these are easily in the top 3.
Easy, quick, delicious- thank you!
I’m so glad to hear all that, Sondrea! I love how quick they are to make! Thanks for taking the time to leave a review!
I just made these for breakfast this morning and they were amazing! Chocolatey, not too sweet and great texture.
I am so glad you loved them, J! Thanks for taking the time to share!
Wow- so good! I made these for my kiddos this morning and they loved them! I made your Butternut squash soup yesterday (also amazing!) and reserved 3/4 cup of the squash (cut into cubes) so I could make these muffins today. I steamed the cubes last night and threw it in the fridge for the night. This morning I put the cubes, the nut butter (I had PB on hand), and the syrup in my vitamin first to get the cubes nice and creamy and more of a purée consistency. They turned out perfectly! These muffins are going to be on regular rotation and I will definitely be sharing the recipe with all of my GF friends! Thank you!!
Meant to say “Vitamix” not vitamin 😆
I am so glad you enjoyed them! Thanks for sharing, Casey!
I have made these muffins many times now and my family all loves them! I use pumpkin purée and sometimes throw in grated zucchini as well.
Hi Kate! I’ve been thinking about how I need to make these muffins again soon now that I have so much butternut squash. I LOVE the addition of the zucchini! How much did you add? I must try.
Probably about a cup. I tell everyone about these muffins and many of your other recipes. Thanks for creating these tasty and nutritious recipes!!