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Home » Recipes » Baking

Whole Wheat Chocolate Chip Muffins

Updated: Oct 8, 2025 · Published: Nov 6, 2024 by Danika Vanderpyl · This post may contain affiliate links · 4 Comments

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On the hunt for healthier chocolate chip muffins? This recipe is made with whole wheat flour, less sugar, and naturally no milk. Perfectly moist and packed with chocolate chips, make these for your next snack time.

I've been making healthy muffins for over 15 years and it's something I bake many times each month! Next, try my popular blueberry muffin recipe without milk, it's another recipe to make when you run out of milk or are avoiding dairy. Or make these decadent chocolate carrot muffins!

A light colored muffins with a lot of chocolate chips poking out of it, sitting on a brown napkin, with other chocolate chip muffins around it.
Jump to:
  • Ingredients needed
  • How to make chocolate chip muffins without milk
  • Tips for whole wheat muffins with chocolate chips
  • Other healthy baking you may like...
  • Whole Wheat Chocolate Chip Muffins
  • Danika Vanderpyl, C.H.N

Ingredients needed

Oil, whole wheat flour, sugar, water, apple cider vinegar, baking soda, baking powder, salt, chocolate chips, vanilla measured out in bowls and 2 eggs on the counter.

Things to know about the ingredients:

  • Whole wheat flour: This recipe uses whole wheat flour to increase the nutrient density in each bite. I only use organic whole wheat flour because as someone who has studied nutrition, I feel this is best for our bodies and our kids. Read more on this here.
  • Oil: Any neutral tasting oil works for these muffins. For the best option for our bodies look for a cold-pressed, organic oil preferably stored in a dark-coloured bottle (to prevent it from going rancid). Such as sunflower oil, grapeseed oil, or melt coconut oil to use. I will say coconut oil will change the taste of the muffins. I haven't tried it but from my baking experience, I believe melted butter would work just fine too!
  • Chocolate chips: In this recipe, I used dark chocolate chips as they contain less sugar and additives and are dairy-free. However, milk chocolate chips can be used of course!

How to make chocolate chip muffins without milk

Follow along with these step-by-step photos from my kitchen. It's kinda like we are making them together.

A glass bowl with yellow liquid in it with a whisk.
  1. Preheat the oven to 425 degrees Fahrenheit. Place all the wet ingredients into a bowl, the eggs, oil, water, vanilla, apple cider vinegar and whisk together.
A wooden bowl with whole wheat flour in it.
  1. In another bowl place the flour, sugar, baking powder, baking soda, and salt. Mix together well.
A wooden bowl with chocolate chip muffin batter in it with a blue spatula in the bowl.
  1. Add the chocolate chips and the egg mixture into the flour mixture and fold together about 12-15 times with a spatula. It's important not to overmix the muffin batter.
Muffin batter in a blue muffin pan.
  1. Line a muffin pan with liners or grease the pan well. Place about ⅓ cup of batter in each muffin cup to fill them all the way up. Sprinkle with coarse sugar or chocolate chips as desired.
    Place the muffin tin in the preheated oven (425 Fahrenheit) to bake for 8 minutes, then turn the oven down to 375 Fahrenheit and bake for another 7-10 minutes, until they are fully baked.

Tips for whole wheat muffins with chocolate chips

  • Don't overmix the batter, only stir the batter about 12 times to get fluffy moist chocolate chip muffins with whole wheat flour. There may be streaks of flour still and it will get mixed in as you fill the muffin cups.
  • Bake at a high temperature to start, 425 Fahrenheit, to create a higher muffin dome, then turn the oven down to 375 Fahrenheit and finish baking them completely.
  • Let the muffins sit for 5 minutes before removing them from the pan. When muffins are still hot they easily break, letting them cool slightly stops them from crumbling.
  • Use cupcake liners. With the big bakery-style tops it makes them easier to remove from the pan without breaking them! I have used silicone liners or paper liners for this recipe. I find when the muffins are in a grease pan or with paper liners they will bake 2-3 minutes faster than when they are in silicone liners.
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A light colored muffins with chocolate chips poking out of it.

Other healthy baking you may like...

Next try my whole wheat chocolate chip cookies! I'm obsessed with making nutrient-dense food for my kids' snacktime. Try these recipes next!

  • Brown banana protein muffins with chocolate chips sitting on a cooling rack beside a plate of chocolate chip muffins.
    Protein Banana Muffins with Oats
  • A brown muffins with green flecks on a cutting board.
    Healthy Zucchini Muffins with Yogurt
  • A basket with a tea towel with muffins that have chocolate chips on top/
    Chocolate Chip Protein Muffins
  • A close up of a morning glory muffin with toasted coconut on top.
    Morning Glory Muffins with Pineapple

Did you make these whole-wheat chocolate chips muffins? Would you take 5 seconds to give a star rating and review just below the recipe? That means a lot to me and helps the growth of Beside the Mountain blog (your email address will not be shown).

A light colored muffins with a lot of chocolate chips poking out of it, sitting on a brown napkin, with other chocolate chip muffins around it.

Whole Wheat Chocolate Chip Muffins

Danika Vanderpyl
A loaded chocolate chip muffin made with whole wheat flour! These are wholesome muffins without compromising the texture or taste. Make them for your next snack!
5 from 1 vote
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 15 minutes mins
Total Time 30 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 274 kcal

Equipment

  • 1 muffin pan
  • 12 muffin liners

Ingredients
  

Dry ingredients

  • 2 cups whole wheat flour
  • ¾ cup white sugar
  • 2 teaspoons baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt

Wet ingredients

  • 2 eggs
  • ⅔ cup oil
  • ⅔ cup water
  • 1 tablespoons apple cider vinegar or lemon juice
  • 2 teaspoons vanilla extract

Add later

  • 1 cup chocolate chips
  • 2 tablespoons optional: turbinado sugar

Instructions
 

  • Preheat the oven to 425.
    Mix wet ingredients: In a medium bowl, place the eggs, oil, water, apple cider vinegar, and vanilla. Whisk together until it is well combined.
  • Mix dry ingredients: In a large bowl mix the dry ingredients, whole wheat flour, sugar, sea salt, baking powder and baking soda. Use a whisk to mix everything well.
  • Fold everything together: Add egg mixture, and chocolate chips into the dry ingredients. Use a spatula to stir the batter together, about 12 folds, just until everything is incorporated. Do not over-stir.
  • Scoop & bake: Add about ⅓ cup of batter to fill each muffin cup. Optionally sprinkle more chocolate chips or with a little turbinado sugar (coarse sugar).
    Place the muffin tin in the preheated oven (425 Fahrenheit) to bake for 8 minutes, then turn the oven down to 375 Fahrenheit and bake for another 7-10 minutes. Remove muffins from the oven when they spring back from the touch and when the center does not look gooey. Let them sit in the pan for 5 minutes before removing.

Notes

Chocolate chips: I like to use mini chocolate chips as they are distributed evenly through the muffin and my kiddos cannot pick them out! However, any chocolate chips works. I also use dark chocolate chips as they contain less sugar and no dairy. 
Read more about which oil or whole wheat flour to use above in the blog post.
Scroll up for step-by-step photos. 
These muffins freeze well. Wait until they are completely cool and then store in a ziplock bag or a sealing container. Place in the freezer for up to 6 months. Read more about the best way to store muffins here. 

Nutrition

Calories: 274kcalCarbohydrates: 26gProtein: 3gFat: 18gSaturated Fat: 4gPolyunsaturated Fat: 4gMonounsaturated Fat: 8gTrans Fat: 0.1gCholesterol: 27mgSodium: 106mgPotassium: 77mgFiber: 1gSugar: 9gVitamin A: 40IUCalcium: 19mgIron: 1mg
Keyword Chocolate chips, Dairy Free Muffins, Healthy Muffins, Whole Wheat Flour
Did you love this recipe?Make sure to leave a comment below!
danika sitting in a chair

Danika Vanderpyl, C.H.N

I create snack recipes with healthy ingredients that are mostly already in your kitchen. I'm certified in Holistic Nutrition and I care about giving my kids real food. Let me share my nutrient-dense easy snacks with you.

Learn more about me →

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Comments

    5 from 1 vote (1 rating without comment)

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    Recipe Rating




  1. Katie says

    November 15, 2025 at 5:56 am

    5 stars
    These just came out of the oven, and look just as you described after baking for the instructed amount of time. The batter was a bit runny, but I’ve noticed that recipes with runny batters make the best cakes/cupcakes/muffins because they stay moist and fluffy. I’m serving these to my daughter’s basketball team (3rd/4th grade), and I know they’ll love them. Thank you for the great recipe!

    Reply
    • Danika Vanderpyl says

      November 17, 2025 at 8:44 am

      Great to hear Katie! This sounds perfect for a basketball team, enjoy!

      Reply
  2. Kat says

    October 01, 2025 at 8:35 pm

    5 stars
    Turned out excellent! I was skeptical because of the apple cider vinegar, I’ve never made a baking recipe that calls for it, but so glad I tried it! I used freshly ground soft white wheat, and for my oil I used half butter and half coconut oil. So fluffy and delicious! This will be our go to muffin recipe now! Thanks so much!!!

    Reply
    • Danika Vanderpyl says

      October 07, 2025 at 1:58 pm

      Awesome to hear you enjoyed these Kat!

      Reply
Danika-vanderpyl-hiking-with-mountains

Hey hey! I'm Danika.

I'm certified in holistic nutrition and I create snack recipes! Because unprocessed, wholesome, nutrient-dense snacks are hard to find but I want everyone to know they are easy to make!

About me

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