Healthy Whole Wheat Chocolate Chip Muffins

Posted: February 14, 2025 Last modified: September 7, 2026
Healthy Whole Wheat Chocolate Chip Muffins

I love to bake little muffins as a treat for myself. These whole wheat chocolate chip muffins are one of my favorites! They do have some sugar with the added honey (and chocolate of course), but overall are pretty healthy.

 

 

Why This Recipe Works

These whole wheat chocolate chip muffins are one of my favorite snacks to bake when I want something a little more wholesome, but still delicious. Here’s why I think you’ll love them too:

  • Quick and easy. The batter comes together in two bowls and the muffins only need 15-18 minutes in the oven.
  • Whole wheat and almond flour. This combination gives the muffins a hearty texture while keeping them tasty and satisfying.
  • Sweetened with honey. There is no refined sugar added to the muffin batter. The sweetness comes from honey and the chocolate chips.
  • Plenty of chocolate. Chocolate chips are folded through the batter and sprinkled on top, so you get chocolate in every muffin.
  • Perfect for freezing. Freeze the muffins individually and you’ll always have an easy homemade snack ready to go.

Healthy or Not?

At first glance, chocolate chip muffins sound like a recipe that can’t possibly be healthy. I’m not saying that these whole wheat chocolate chip muffins are the most healthy muffins out there, but using a whole grain batter as the base makes them much more nutritious.

Whole wheat flour fills you up quicker and keeps you fuller for longer. As a result, you are less likely to reach for a second muffin after the first. In terms of taste they are still absolutely delicious so using whole wheat flour is simply a way to make them a little better for you.

To make them even more healthy, you could switch the milk chocolate chips to (sugar free) dark chocolate. And the honey could be substituted with another sweetener.

Do you prefer to make muffins without whole grain flour? Try these vanilla muffins or these delicious apple cinnamon muffins.

Whole Wheat Muffins

Have you ever made whole grain muffins? I’ve got the hang of them now and can’t get enough. Maybe I should also try to make a recipe for whole wheat cupcakes, but for now you can start with these whole wheat chocolate chip muffins.

There is much less sugar in these muffins and the only sweetness comes from the chocolate and the honey. No refined sugar is added to the muffin batter.

Not sure what the difference is between muffins and cupcakes?

Whole wheat chocolate chip muffins-1

Recipe Ingredients

  • whole wheat flour – while the taste will be different you can substitute with all purpose flour or use half/half
  • almond flour
  • baking powder
  • egg
  • whole milk
  • sunflower oil – or use a mild olive oil or coconut oil
  • dark chocolate chips – or a bar of chocolate, chopped in little pieces
  • vanilla extract
  • honey

Other than those ingredients you will need a muffin tin to make these healthy chocolate muffins. You don’t really need a food processor for this recipe as the mixing of the wet ingredients and the dry ingredients is super easy and doesn’t require long mixing.

You first mix the dry ingredients in a large bowl and mix the wet ones in another bowl. Combine the two together and you’re done.

Divide the batter over the muffin pan (lined with paper liners) and bake in the oven in around 15-18 minutes or until golden brown. Place them on a wire rack to cool completely

the best applesauce muffins

Vanilla muffin recipe

Variations

Now if you want to make some variations or go for a dairy free muffin you can replace the whole milk with a plant based alternative.

If you want you can replace the honey for coconut sugar or brown sugar as the amount is not that big and it should be possible without too much trouble with the batter. Keep in mind that I have not tested the recipe with the coconut sugar. But maple syrup should be an easy swap.

I find that these delicious healthy chocolate chip muffins make for easy healthy snacks. Perfect for a lunch break or snack in between meals.

I like to freeze them in single pieces in a ziplock bag so I always have a perfect snack ready to go.

How to store whole wheat chocolate chip muffins

These whole wheat chocolate chip muffins are perfect for making ahead. Let the muffins cool completely before storing them and keep them in an airtight container so they stay fresh.

How long do whole wheat chocolate chip muffins last?

Store the muffins in an airtight container outside of the fridge, once they have cooled completely. If you want to keep them for longer, I recommend freezing them.

Can I freeze whole wheat chocolate chip muffins?

Yes, these muffins freeze very well. I like to freeze them individually in a ziplock bag, so I can easily take out one whenever I feel like a homemade snack. They will keep in the freezer for up to three months. Let the muffin thaw before serving.

Some More Delicious Muffins!

Of course you will find plenty more easy and delicious muffin recipes on the In Laura’s Bakery site. A few favorites:

FAQ Whole Wheat Chocolate Chip Muffins

Can I use all-purpose flour instead of whole wheat flour?

Yes, you can substitute the whole wheat flour with all-purpose flour. You could also use half whole wheat and half all-purpose flour. Keep in mind that this will change the taste and texture of the muffins.

Can I make these muffins dairy free?

You can replace the whole milk with your favorite plant-based alternative. This makes it easy to adapt the muffins if you prefer not to use dairy.

Can I replace the sunflower oil?

Yes. You can use a mild olive oil or coconut oil instead. Choose an oil with a mild flavor so it doesn’t overpower the other ingredients.

Can I replace the honey?

Maple syrup should be an easy substitute for the honey. Coconut sugar or brown sugar may also work, although I haven’t tested the recipe with coconut sugar.

Can I use a chocolate bar instead of chocolate chips?

Absolutely. Simply chop your favorite chocolate bar into small pieces and use these instead of chocolate chips.

 

Whole wheat chocolate chip muffins

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Whole wheat chocolate chip muffins

These chocolate chip whole wheat muffins are so delicious. And a little more responsible than the regular muffin. Win-win!
Preparation15 minutes
Cooking15 minutes
Total30 minutes
Servings: 10 pieces

Ingredients 

  • 150 grams whole wheat flour
  • 50 grams almond flour
  • 1 tsp baking powder
  • Pinch salt
  • 1 egg
  • 125 ml milk
  • 60 ml sunflower oil
  • 1 tsp vanilla extract
  • 2 tbsp honey
  • 100 grams chocolate chips or a chopped bar

Equipment

  • Muffin pan
  • Paper liners

Instructions

  • In a bowl mix the whole wheat flour, almond flour, baking powder and salt.
  • In a second bowl, whisk together the egg, milk, sunflower oil, vanilla extract and honey.
  • Pour into the dry ingredients and mix with a spatula until the dry ingredients are incorporated. Finally, fold 80g (2.8 oz) of the chocolate chips into the mixture with a spatula.
  • Pour the mixture into the muffin pan and sprinkle the remaining chocolate chips on top.
  • Bake the muffins at 200°C/400˚F (conventional oven) for 15-18 minutes.
Tips

To make them healthier, you can replace the (milk) chocolate with dark chocolate, or replace the chocolate altogether with pieces of fruit or nuts.
How to store

Keep out of the fridge for 4-5 days. Can be frozen for up to three months in an airtight container.

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