Best Ever Healthy Chocolate Chip Muffins

Soft and tender crumb with sweet vanilla and loads of chocolate chips for the best ever healthy chocolate chip muffins recipe!

Welcome to the Best EVER Healthy Chocolate Chip Muffins recipe. Throw away all of your other healthy chocolate chip muffins recipes. Heck, throw away all of your traditional chocolate chip muffins recipes.

This one is all you’re gonna need.

When baking and baking rounds of healthy muffins in the Beaming Baker Test Kitchen (oooh, sounds so official!), Erik and I were halted in our tracks when we tasted today’s healthy chocolate chip muffins.

We stopped production (aka home baking lol), called anyone and everyone we knew, and demanded everything stop for one second so we could all happily sigh over how friggin’ amazing these healthy chocolate chip muffins turned out.

Hint: they taste like the best ever chocolate chip cookies in muffin form. And they just happen to be healthy. Say whaaaa???

Try your hand at making super-duper-secretly healthy chocolate chip muffins and WOW all of your friends and fam with the shocker factoid that these babies are actually healthy. *Mic drop*

Ready to get into today’s baking adventure? Let’s do it!

Chocolate chip muffins on parchment paper and cloth in a tray, with a single muffin stacked on top

How to Make Healthy Chocolate Chip Muffins

I love making these healthy chocolate chip muffins because they’re so easy to bake, and yield a super tender muffin packed with guilt-free chocolate chip delight!


Firstly, preheat the oven to 350°F. Line a 12-cup muffin pan with muffin liners.


Secondly, in a large bowl, sift together oat flour, almond flour, baking soda, baking powder and salt. 


Next up, heat up the water and milk until just warm—this keeps the coconut oil from solidifying once combined.

Whisk the Wet Ingredients

In a medium bowl, whisk together all of the wet ingredients until well mixed: water, milk, lemon juice, coconut oil, coconut sugar, maple syrup and vanilla. 


Whisk together the wet and dry ingredients.

Pour Batter

Pour batter evenly into the prepared muffin pan. Top with chocolate chips. 

Bake, Cool and Enjoy

Bake for about 29 minutes. Cool and enjoy the best ever healthy chocolate chip muffins!

My favorite chocolate chips muffins ever—they just happen to be healthy. Deep vanilla flavor with a buttery profile and sweet, dark chocolate chips balancing it all out beautifully.

Chocolate chip muffins on parchment paper

Healthy Ingredients for Healthy Chocolate Chip Muffins 

Oat Flour

Remember the days when you had to put a clothes pin over your nose and force yourself to eat too many bowls of tasteless oatmeal? Forget all of those days by using fiber-rich, heart-healthy oat flour instead of highly processed, bleached all purpose flour to make these healthy chocolate chip muffins. Oat flour: keeps you regular and satisfied with yummy healthy chocolate chip muffins! Learn How to Make Homemade Oat Flour here.

Almond Flour

I simply love sneaking almonds into my healthy recipes because they provide an added boost of healthy fats, nutrients and keep you satisfied longer. Whole ingredients = whole belly (that’s actually full.) Here is the almond flour that I use.

Coconut Oil

One of my favorite healthy ingredients to use in my healthy baking recipes. Coconut oil contains healthy fatty acids that raise good cholesterol in your blood, which can, in turn, reduce heart disease, and provide quick energy stat!

Coconut Sugar & Maple Syrup

My favorite refined sugar-free sweeteners that retain nutrients like iron, zinc, calcium and potassium and antioxidants. You can find coconut sugar here.

Refined Sugar-Free Chocolate

Try these paleo chocolate chunks that are vegan, gluten free and refined sugar-free. Keeping your sugar low? Use these stevia-sweetened sugar-free chocolate chips instead. 😉

Healthy Muffins You Might Like

The Taste & Texture

Texture: These healthy chocolate chip muffins are super moist, rich with a soft, tender crumb that’s perfectly fluffy. You’d never guess these chocolate chip muffins were healthy!

Taste: No exaggeration, these muffins taste exactly like chocolate chip cookie dough, in muffin form! Sweet vanilla flavor, bursting with melty morsels of delicious chocolate chips. Deep vanilla flavor with buttery profile and sweet & dark chocolate chips balancing it all out.

Unbelievably good healthy chocolate chip muffins! Rich chocolate flavor, soft & moist crumb and gorgeous notes of vanilla.

Angled shot of healthy chocolate chip muffins in a tray with parchment paper and cloth, with a single muffin stacked on top of the rest

Ingredient Substitutions

  • Oat Flour: some folks have swapped the oat flour in this recipe with whole wheat flour, all purpose flour and even gluten free all purpose flour with success. I love oat flour the best, but you can try the all purpose or wheat flour you have on hand. And in case you’re interested, try your hand at learning how to make oat flour.
  • Almond Flour: try keeping this sub as similar as possible. For example, use cashew flour or sunflower seed flour. If you don’t have any of those on hand, you *might* be able to use an additional ¼ cup oat flour. I’ve tried this sub in the past with a few different muffin recipes with success. However, keep in mind that the best results come from sticking to the recipe. 😉
  • Coconut oil: here, melted vegan butter or any kind of butter will work.
  • Coconut Sugar: try using brown sugar.
  • Maple Syrup: you can try using brown rice syrup, honey or another liquid sweetener. As with all recipes, keep in mind that any swaps may result in an unexpected texture. Try your swap and see how you like the results, then adjust accordingly.
  • Chocolate Chips: feel free to swap the chocolate chips in these healthy muffins with your favorite add-ins, such as fruit, nuts and seeds. Just make sure to keep the proportions the same.

Delicious Pairings for Your Healthy Muffins

Okay, so now you’re all set with making these healthy muffins every freaking day–but how to shake things up? I love adding toppings on my healthy muffins in order to change up their flavor profile. Try these out! 🙂

  • Top with nut butter
  • For a dessert treat, serve with healthy ice cream
  • Coconut whip

a stack of healthy chocolate chip muffins cooling on parchment paper with more chocolate chips muffins

Great Tools for the Best Healthy Chocolate Chip Muffins

  • Almond Flour: this almond flour is super finely ground and blanched, making for amazing flour-like quality in these chocolate chip muffins.
  • Try these paleo chocolate chunks that are vegan, gluten free and refined sugar-free. Keeping your sugar low? Use these stevia-sweetened sugar-free chocolate chips instead. 😉
  • Unbleached Muffin Liners or Nonstick Parchment Muffin Liners: I love both of these and swap which ones I use from time to time. The unbleached ones are compostable and stick just-enough to the muffins while the nonstick ones will literally fall off after cooling (perfect for those who hate liners that stick!).
  • Large Scoop: for super easy muffin batter distribution. I love using this large scoop to distribute muffin batter quickly and evenly to each muffin cup.

Are you ready to have your muffin-print socks blasted off!? I mean, these healthy chocolate chip muffins are that good. Try your hand at making them, and let me know what you think in the comments below! I’m so grateful that you’re here, sharing in these baking adventures with me and the fam. ‘Til the next one…

Sending you all my love and maybe even a dove, xo Demeter ❤️

🍫 📸 🍫

📸 Did you make this healthy chocolate chip muffins recipe? Take a pic and share it on Instagram with the hashtag #beamingbaker & tag @beamingbaker. I’d love to see it! 📸

More Healthy Chocolate Muffins

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Best Ever Healthy Chocolate Chip Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 13 reviews


BEST EVER Healthy Chocolate Chip Muffins: soft & tender muffins with a perfectly moist and fluffy crumb, sweet vanilla flavor, and bursting with melty chocolate chips. Tastes like chocolate chip cookies in muffin form!



Dry Ingredients

Wet Ingredients

  • ½ cup + 2 tablespoons water
  • ½ cup non-dairy milk
  • 1 tablespoon lemon juice
  • 3 tablespoons melted coconut oil
  • ¼ cup coconut sugar
  • ¼ cup pure maple syrup
  • 1 teaspoon pure vanilla extract

Add-in Ingredients

Optional Topping


  1. Preheat oven to 350°F. Line a 12-cup muffin pan with muffin liners. Set aside.
  2. In a large bowl, sift together all the dry ingredients: oat flour, almond flour, baking soda, baking powder and salt.
  3. Add water and milk to a microwave-safe bowl. Heat in 10-second increments until just warm. This will prevent the melted coconut oil from solidifying once mixed with these liquids.
  4. In a medium bowl, whisk together all wet ingredients: water, milk, lemon juice, coconut oil, coconut sugar, maple syrup and vanilla. Whisk until well incorporated.
  5. Add wet ingredients to dry ingredients. Whisk until just incorporated, making sure no flour patches remain. Fold in chocolate chips.
  6. Pour batter evenly into prepared muffin pan—I spread mine into 10 muffin cups for large, full muffins, but you can do 12. Optionally, top with chocolate chips. Lightly press chips into batter.
  7. Bake for 26-32 minutes. Mine took 29 minutes. Insert a toothpick to check for doneness—once it comes out clean, it’s done. Place muffin pan on a cooling rack to cool for 30 minutes. Gently remove muffins from muffin pan and transfer to a cooling rack to cool completely, about 1.5 hours. Enjoy! Storing instructions below.

More Healthy Chocolate Chip Muffins





Where to Buy Ingredients:

A Note on Homemade Oat Flour: *If using homemade oat flour, make sure to blend the flour until very fine and sift the flour to remove coarse bits of oats that could create less than ideal results. Store until needed, then measure the amount required for the recipe.

Storing Instructions: Store in an airtight container for up to 1 week in a cool, dark environment.

To Freeze: Store in an airtight container or bag, in the freezer for up to 1-2 months. Allow to thaw for about 30 minutes at room temperature before enjoying. Or, heat in the microwave in 10-second increments until just warm.

Recommended Tools: Large ScoopUnbleached Muffin Liners or Nonstick Parchment Muffin LinersMuffin Pans (2pk)

  • Prep Time: 25 mins
  • Cook Time: 29 mins
  • Category: Dessert, Breakfast, Snack
  • Method: Bake
  • Cuisine: American

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  1. Hi Demeter: Awesome recipe!! Trying to use some over-ripe bananas and wondering if they would be an even swap with the coconut sugar and maple? Same quantity? Thinking 1-2 bananas would be enough for 1/2 cup? Would love to make these tomorrow morning!! Thx— love your recipes and writing style!! 😃

  2. I haven’t tried this receipe yet but I have tried some of your other recipes. They are great. I have a question I cannot have almond flour so how much more oat flour would I need to substitute. I haven’t gotten any emails about receipes from you in awhile hope all is well

    1. Hi Maros! I’d say to swap the almond flour with 6 tablespoons oat flour, though it will have a bit of a different texture. Not sure why you haven’t been getting the emails. Maybe check your spam filter?

  3. I don’t have coconut sugar and like things on the less sweet side- would it be ok to leave it out and just use the 1/4 cup of maple syrup?

    1. Hi Sasha. I would not recommend leaving the sugar out completely as it will affect the texture and taste of the muffins quite a bit. You could try swapping it for organic brown sugar, though I haven’t tried that specific sweetener in this recipe myself. If you do, let me know how it goes! 🙂

      1. Thank you! I’ll try the original recipe and see how it goes 🙂 Are these muffins very sweet as written?

  4. Hi Demeter
    I was wondering what be substituted for the almond flour? Extra oat but how much? I love your recipes have made several of them they are all great and tasty. Can you maybe someday have a recipe for scones and fresh baked bread for sandwiches.
    Thank you
    Be Well and Safe

    1. Hi Maria, try subbing the almond flour with 1/4 cup extra oat flour. The muffins won’t be as light and fluffy, but should be pretty close. I’ll add your recipe requests to an ongoing list of recipes to develop. 🙂 Be well and safe too! Sending you big hugs.

  5. If someone can’t have almonds, could I substitute another flour for the almond flour? Maybe walnut flour? Thanks!

  6. I loved every one of these ingredients! I think almond flour is the best gluten free flour and the muffins backed up so nice. Thank you!

      1. Hi
        I loved it 😍 .
        Are the cups used the same as that we use in the standard standards and what can we use instead of coconut sugar & maple syrup?

      2. Hi Rasha! So happy you enjoyed the muffins! All the measurements are made using standard US measurements. As for the sweeteners, I’ve had other readers use brown sugar or date sugar in place of the coconut sugar and honey or brown rice syrup in place of the maple syrup. I haven’t tried it myself in this recipe, so I can’t say for sure. Let me know how it goes!

      3. I am going to try this recipe out today, but I am curious about the tablespoon of lemon juice — I wouldn’t have expected that in a chocolate chip muffin recipe? Does it add a lemon flavor to the muffin? Or is it there for another reason? Thank you so much.

  7. I definitely need these in my life! A healthy chocolate chip muffin that tastes amazing? What’s not to love!

  8. I’m feeling very lucky because I have all the ingredients in the kitchen now to make these muffins. The texture looks perfect!