Healthier Oatmeal Chocolate Chip Muffins

There’s nothing better than waking up to the smell of freshly baked muffins.

Vertical image of a cooling rack with rows of muffins studded with dark chips, with text on the top and bottom of the image.

When I was growing up, my mom often made chocolate chip muffins several times a week. And those mornings were always the best.

I’d get out of bed, stumble my way downstairs, and find a bowl of leftover batter waiting for me, to polish off while the treats finished baking.

Now, these weren’t like the healthier homemade muffins in this recipe. We’re talking sugar-filled ones that were so fluffy and sweet – essentially cupcakes without the frosting.

I’d take one, along with a big glass of milk, flip it upside down, and eat the muffin from the bottom up, leaving the gooey top for last.

Vertical image of three rows of oat baked goods on a cooling rack on a white surface.

While this whole grain recipe is far more nutritious than the chocolate chip goodies of my childhood, I still prefer to save the tops for last.

As a dietitian, I’m now much more conscious of what I eat. But that doesn’t mean I want to sacrifice my favorite foods either. Instead, I’m all about finding ways to make my favorite recipes healthier.

These oatmeal chocolate chip muffins are a slightly healthier take on the bakery classic.

First, instead of white all-purpose flour, we’re using white whole wheat flour and old fashioned oats.

Oats are a whole grain that has been associated with a handful of health benefits, as they’re an excellent source of fiber.

Vertical close-up image of round baked goods studded with oats and chocolate on a cooling rack on a white surface.

White whole wheat flour is made from white rather than red whole grain wheat. As a result, it has a lighter color than traditional whole wheat flour.

But what I love most about white whole wheat flour is that you still get all the nutritional benefits of eating whole wheat, but with a softer texture that more closely resembles products made with refined all-purpose flour.

To help cut back on sugar and fat, these are also made with unsweetened applesauce.

While there’s still oil and brown sugar in the recipe, applesauce helps to cut back on the total quantities of these a bit, while providing an extra boost of fiber.

To compare, a traditional bakery-style chocolate chip muffin can have as much as 28 grams of sugar, whereas the ones in this recipe have about 16 grams each.

Vertical image of rows of chocolate chip baked goods on a cooling rack, with one cut in half.

That’s still more than I’d eat as an everyday breakfast, but for a special weekend treat, it’s much better than store-bought! Plus, the fiber from many of the other ingredients can help slow the absorption of sugar, meaning a potential reduction of spiking blood sugar levels.

Finally, we’re also adding flax seeds. In addition to adding fiber, these are an excellent source of healthy fats. In fact, after chia seeds, flax seeds are one of the best plant sources of omega-3 fatty acids.

While you may have heard of omega-3s before, I’ll recap briefly: this is a type of fat that our bodies can’t make on their own. Instead, we have to get them through our diets. They help with brain and eye health, as well as reducing inflammation in the body.

Have I convinced you yet that, nutritionally at least, you need these muffins? If so, then let’s talk about why your taste buds need them too!

Vertical image of a baked good cut in half next to a glass of milk and a yellow napkin.

Slightly nutty thanks to the oats, they have a soft texture with rich bites of chocolate sprinkled throughout. Plus, they aren’t overly sweet, making them perfect for breakfast or a healthy snack.

To get the most out of each chocolatey bite, I highly recommend eating them hot from the oven, or microwaving one for a few seconds before eating. After all, there’s nothing better than warm, melted chocolate.

So, treat yourself to a warm, oat-filled homemade baked good for your next breakfast or snack. Bonus points if you save the muffin top for your last few bites!

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Horizontal image of three rows of oat and chocolate baked goods on a cooling rack on a white surface with scattered grains.

Healthier Oatmeal Chocolate Chip Muffins

  • Author: Kelli McGrane
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x


Healthier oatmeal chocolate chip muffins are made with whole wheat flour and applesauce for a nutritious spin on a bakery favorite.


  • 1/4 cup melted coconut oil, or canola oil 
  • 1/2 cup low-fat milk, or dairy-free milk alternative 
  • 2 large eggs
  • 1/2 cup packed light brown sugar
  • 4 ounces unsweetened applesauce
  • 3/4 cup old fashioned oats
  • 1 1/2 cups white whole wheat flour
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt
  • 2 tablespoons ground flax seeds 
  • 1/2 cup dark or semi-sweet chocolate chips


  1. Preheat oven to 350°F. Lightly grease or line a 12-cup muffin pan. 
  2. In a large mixing bowl, whisk together oil, milk, eggs, brown sugar, and applesauce until well combined. Set aside. 
  3. In another mixing bowl, combine oats, flour, baking soda, salt, and ground flax. 
  4. Slowly stir flour mixture into the wet ingredients until just combined. 
  5. Pour batter into prepared muffin tin, filling each cup about ⅔ of the way full. 
  6. Place pan in the oven and bake for 20 minutes, or until a toothpick inserted in the center comes out clean.
  7. Remove pan from the oven and set aside to cool for 5 minutes. Gently remove muffins from pan and place on a cooling rack to cool completely. Store in an airtight container for 3-5 days.
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Category: Muffins
  • Method: Baking
  • Cuisine: Baked Goods

Keywords: muffin, chocolate chip, oatmeal, whole wheat flour, flax seed

Cooking By the Numbers…

Step 1 – Preheat Oven and Measure Ingredients

Preheat your oven to 350°F. Lightly grease a muffin pan with oil or cooking oil spray. Alternatively, you can use individual paper muffin liners.

Horizontal image of assorted wet and dry ingredients in small glass bowls next to two eggs on a white surface.

Melt the coconut oil and allow it to cool slightly. Measure out all of the remaining ingredients.


  1. Canola or olive oil can be substituted for the melted coconut oil to slightly reduce the amount of saturated fat. Just note that olive oil may slightly affect the flavor.
  2. You may also use a milk alternative, such as oat or almond, in place of the lowfat milk.
  3. You can use a store-bought unsweetened applesauce, or one of our recipes for a stovetop or pressure cooker version. Omit any sugar and seasonings from the recipes.

Step 2 – Make Batter

Set out two mixing bowls: one small and one medium-sized.

In one, whisk together the oil, milk, eggs, granulated sugar, and applesauce until well-combined. Set aside.

Horizontal image of a thick light brown chunky batter in a large glass bowl stirred by a spoon.

In the second bowl, stir together the oats, flour, baking soda, salt, and ground flax seeds.

Slowly stir the flour mixture into the wet ingredients until just combined. You don’t want to overmix your batter, otherwise your muffins may become too dense.

Gently fold in the chocolate chips.

Step 3 – Bake

Evenly distribute batter into the muffin pan, filling each cup about 2/3 full.

Horizontal image of baked muffins in a pan.

Bake for 20 minutes, or until an inserted toothpick comes out clean.

Step 4 – Cool and Serve

Remove from the oven and allow the muffins to cool in the pan for 5 minutes.

If you used liners, simply remove the muffins from the pan and place them on a cooling rack until fully cooled.

Horizontal image of a knife removing a baked muffin from a pan.

If you didn’t line your pan, gently run a butter knife between each muffin and the tin to help unstick them. Carefully remove each muffin from the pan, and place on a cooling rack.

Enjoy immediately, or cool completely before storing.

Too Many Muffins? Freeze ‘Em!

While twelve muffins may be just the right number if you have a large family, several roommates, or coworkers to help eat them, for just one or two people it may be hard to get through all of them in a few days.

That’s where freezing comes in.

To freeze these muffins, allow them to cool completely first. Place them in a large freezer bag labeled to indicate what’s inside and the date when they were made, and freeze for up to three months.

Horizontal image of three rows of oat and chocolate baked goods on a cooling rack on a white surface with scattered grains.

To thaw, you can simply place one or two out on the counter and allow them to come to room temperature. This should take about 30-45 minutes, depending on how warm your kitchen is.

However, my favorite way to reheat frozen muffins is to place one on a plate and microwave it for 20-30 seconds. Instead of simply being thawed, microwaving gives them that hot-from-the-oven melted chocolate vibe that I just can’t get enough of.

Looking for more muffin recipes with a healthy twist? Try one of these next:

Do you have a childhood favorite food that you’ve found a way to make healthier? Share in the comments below. Love this recipe? Let us know by leaving a 5-star rating!

Photos by Kelli McGrane, © Ask the Experts, LLC. ALL RIGHTS RESERVED. See our TOS for more details. Originally published on January 15, 2012. Last updated August 24, 2020.

Nutritional information derived from a database of known generic and branded foods and ingredients and was not compiled by a registered dietitian or submitted for lab testing. It should be viewed as an approximation.

The written contents of this article have been reviewed and verified by a registered dietitian for informational purposes only. This article should not be construed as personalized or professional medical advice. Foodal and Ask the Experts, LLC assume no liability for the use or misuse of the material presented above. Always consult with a medical professional before changing your diet, or using supplements or manufactured or natural medications.

About Kelli McGrane, MS, RD

Kelli McGrane is a Denver-based registered dietitian with a lifelong love of food. She holds undergraduate and master’s degrees in nutrition science from Boston University. As a registered dietitian, she believes in the importance of food to nourish not only your body, but your soul as well. Nutrition is very personal, and you won’t find any food rules here, other than to simply enjoy what you eat.

2 thoughts on “Healthier Oatmeal Chocolate Chip Muffins”

  1. I love oaty muffins! They just taste so, I don’t know, raw? Basic? Unadulterated? Unprocessed? Anyhow, these were very good.


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