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Healthy Chocolate Chip Muffins

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Healthy Chocolate Chip Muffins made with whole grain flour, sweetened with maple syrup and dairy-free too. Basically, lightened up bakery style muffins!

muffin on a plate with chocolate chips

Why You’ll Love These

You know the chocolate chip muffins you see at the coffee shop? Well these are kind of like that. BUT:

  • Lightened up a touch
  • Made with whole grain flour
  • Sweetened with maple syrup
  • Dairy free using non-dairy milk.

Plus, you can even make these vegan friendly by using a flaxseed egg.

What’s not to love?

Bakery Style Chocolate Chip Muffins

muffin sliced open on a plate topped with butter

A classic recipe with some healthier swaps – ingredients you likely already have in your pantry!

Muffin Ingredients

  • whole wheat pastry flour, or a mix of whole grain flours.
  • baking powder and salt
  • non-dairy milk, use something like oat milk or hemp milk to keep this recipe nut free. Or use almond milk, cashew milk or coconut milk.
  • eggs & oil, for structure and moisture. Feel free to use light olive oil, sunflower oil or avocado oil. If using coconut oil, just make sure the rest of your ingredients are room temperature or the coconut oil will solidify.
  • maple syrup, for the unrefined sweetener. If you want a sweeter muffins, you can add a few more tablespoons of granulated sugar.
  • vanilla, for flavor
  • chocolate chips, of course. I like to use a mix of mini and regular sized morsels.

Quick & Easy Recipe

I love muffin recipes – they’re fast to make and ready to eat within 30 minutes.

All of the ingredients are easily mixed by hand and distributed into a muffin tin – grease, use paper liners or silicone liners <– I love these!

Bake for about 15-20 minutes and you have yourself the most delicious whole grain healthy chocolate chip muffins that happen to be dairy-free too.

  • eggs in mixing bowl
  • chocolate chip muffins batter

Hot to get Higher Muffin Tops

Bake the muffins at 425ºF first for 5 minutes. The high heat will help create higher rise. After 5 minutes, keep the muffins in the oven, drop the temperature down to 350ºF and continue baking for another 10 minutes or so.

High muffins tops for the win!

muffins in a baking pan

Vegan Version (Egg Free)

If you’re looking to make this recipe egg-free, just mix 2 tablespoons of milled flaxseed (ground flaxseed) with 1/3 cup of water and allow the mixture to gel up for about 5 minutes.

Mix in the flaxseed “eggs” with the rest of the wet ingredients, following the directions as normal.

Freezing Muffins

Allow muffins to cool completely before storing in an airtight container and place in the freezer, up to 3 months.

Allow muffins to thaw at room temperature.

muffins on a black circle cooling rack

I personally prefer these muffins served warmed and with a little bit of butter – so good!

More Muffins to Love

Let me know if you make this recipe by leaving a comment and rating below! It helps others learn more about the recipe too! Xx, Ashley

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Healthy Chocolate Chip Muffins

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★★★★★

5 from 2 reviews

Simple Healthy Chocolate Chip Muffins made with whole grain flour and dairy-free too. This recipe is great for kids! 

  • Author: Ashley
  • Prep Time: 5 minutes
  • Cook Time: 20 minutes
  • Total Time: 25 minutes
  • Yield: 12 muffins 1x
  • Category: snacks
  • Method: oven
  • Cuisine: american

Ingredients

Scale
  • 2 cups whole wheat pastry flour *(or 1:1 gluten-free all-purpose)
  • 2 tsp baking powder
  • 1/4 tsp salt
  • 1/2 cup oil (avocado, light olive, sunflower)
  • 1/3 cup maple syrup
  • 3–4 Tbsp granulated sugar, optional
  • 2 tsp vanilla extract
  • 2 large eggs, room temperature**
  • 2/3 cup non-dairy milk
  • 3/4 cup mini chocolate chips
  • coarse sugar for sprinkling tops

Instructions

  1. Preheat oven to 425ºF. Grease 12 muffin cups or use silicone liners. Set aside.
  2. In a medium bowl whisk together flour, baking powder and salt. Set aside.
  3. In a large bowl whisk together oil with maple syrup, add in eggs and vanilla, whisk until combined. 
  4. Add bowl of dry ingredients into large bowl of wet ingredients. Gently begin to combine then add in milk and stir until ingredients are almost incorporated. Gently fold in chocolate chips, being careful not to over-mix. Batter will be somewhat thick. Avoid over-mixing the batter or you’ll end up with tough muffins.
  5. Evenly distribute batter into 12-cup muffin pan, filling 2/3 full (I like to use a medium cookie scoop). Sprinkle on more mini chocolate chips if you’d like and top with pinches of coarse sugar.
  6. Bake muffins at 425ºF for 5 minutes, then reduce oven temperature to 350ºF and continue baking for an additional 10-12 minutes, or until inserted toothpick in center of muffin comes out clean. Allow muffins to cool in pan for about 10 minutes before gently removing. TIP: if greasing muffin pan, I use a butter knife to remove from pan.
  7. Transfer chocolate chip muffins to wire rack and allow to cool completely before storing. Muffins are best enjoyed fresh within 3 days. These muffins are a little bit more dense than traditional muffins but still delicious! They taste amazing warmed up with a little bit of butter.

Equipment

Notes

*FLOUR  – Whole wheat white flour OR half all-purpose half whole wheat flour OR 1:1 gluten-free all-purpose flour will be fine. I did not test with grain-free flours. If looking for grain free muffins, try these.

*TO MAKE VEGAN – Sub eggs with 2 Tbsp flaxseed meal + 1/3 cup water; let mixture gel up for 5 minutes. I haven’t tested the egg free version with the 1:1 gluten free flour, so if trying this way, the results may differ.

Feel free to half the batch if you’d like less muffins.

recipe slightly updated in 2021 for better results and vegan version.

Nutrition

  • Serving Size: 1 muffin
  • Calories: 223
  • Sugar: 14
  • Sodium: 194
  • Fat: 11
  • Saturated Fat: 8
  • Unsaturated Fat: 0
  • Trans Fat: 0
  • Carbohydrates: 28
  • Fiber: 3
  • Protein: 4
  • Cholesterol: 16

Keywords: healthy chocolate chip muffins, healthy muffin recipes, dairy free muffins

About Ashley

"Ashley Walterhouse is the founder of Fit Mitten Kitchen, based in the Greater Lansing Area of Michigan, AKA “the Mitten.” Ashley grew up as a picky eater but later discovered that eating healthy was actually easy and fun. She started FMK in 2015 as a way to share her newfound love of developing healthier recipes for all to enjoy."

Reader Interactions

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    • Ashley says

      2/3 cup! When I tested the recipe I felt it needed a touch more milk so I must have forgot to go back to the actual instructions. Thank you for letting me know! Will fix 🙂

      Reply

      • Kate says

        I replaced the oil with apple sauce to make them a bit more healthy. I also used 1 cup whole wheat and 1 cup all purpose flour (as suggested in the notes). I followed the baking instructions perfectly and got an amazingly crunchy top and soft middle. Yum!

        Reply

  3. Sarah says

    Amazing recipe! Honestly can’t believe the much healthier ingredients! Going to be making twice in one week 😊. Lots of amazing recipes on this site!

    ★★★★★

    Reply

  4. Kendra says

    These turned out SO GOOD. I loved that they are made with whole wheat pastry flour so they are soft and fluffy. I got the perfect muffin tops with this recipe and the flavor is awesome. They taste just like a warm gooey chocolate chip cookie.

    ★★★★★

    Reply