These Healthy Chocolate Chip Muffins are packed with protein and nutrients. They’re the perfect, guilt-free way to satisfy your sweet tooth in the morning, and the added plant-based protein will help you to feel full until your next meal. These healthy muffins can be made regular-sized, mini, or even in a loaf pan.

My youngest has been really into the packaged, mini chocolate chip Entenmann’s muffins for a while now. They’re convenient, so I do buy them sometimes, but I’ve been wanting to develop a healthier alternative for him. My Chocolate Chip Muffins are packed with tons of nutritious ingredients, including plant-based protein powder, flaxseed, eggs, and Greek yogurt. I’m happy to report that he loves this new, healthier version!
Why You’ll Love This Healthy Muffin Recipe
- Great for breakfast or snacks – Muffins are one of those foods that can be enjoyed for breakfast, snacks throughout the day, or even dessert. I try to use unrefined sugars and like to pack them with healthy ingredients, like flaxseed, protein powder, and whole wheat flour, so they give you energy while also helping satisfy your sweet tooth.
- Easy to make – I love making muffins because the batter comes together in about 15 minutes, and all the ingredients can be mixed in one bowl. This muffin batter can be used for regular-sized muffins, mini muffins, or even a loaf.
- Made with healthier ingredients – These muffins do have regular muffin ingredients, like sugar, oil, and chocolate chips, but I try to swap in as many nutritious ingredients as I can. I like to use unrefined sugar, like coconut sugar and maple syrup. I also add in a few tablespoons of ground flaxseed and pea protein powder for an extra boost. You can also use whole wheat flour, or even just a mixture of whole wheat and all-purpose.

Perfect Muffin Recipe Tips
- If not using muffin liners, make sure to grease your muffin tin well so the muffins come out easily after baking.
- Use room temperature ingredients. I don’t always do this myself, but baking recipes do tend to work better if all ingredients are at about the same temperature when mixed. This primarily refers to the eggs, milk, yogurt, and maple syrup.
- Let the batter sit for about 15 minutes after it’s all mixed, then scoop it into the muffin tin and place it in the oven. This will allow the flour to hydrate more, and the leveners, like baking powder, will work more effectively.
- Don’t overmix the batter. The more you mix the muffin batter, the less fluffy the muffins will be. Overmixing the batter allows the gluten to develop further, leading to a tough, dense muffin.

Healthier Chocolate Chip Muffin Recipe Ingredients
- Eggs – I used two large eggs in this muffin recipe. They add protein and improve the muffins’ texture. I made this recipe with a vegan egg substitute, and it worked well, though the texture is a bit less firm.
- Oil – I’ve made this recipe using canola oil and coconut oil. You want an oil that is liquid at room temperature, and that won’t add too much flavor to the muffins. If using coconut oil, make sure to use refined coconut oil to avoid a strong taste.
- Sweetener – These chocolate chip muffins are sweetened with pure maple syrup and coconut sugar. You could instead use brown sugar and honey as substitutes, if needed. Vanilla extract and cinnamon also help add sweetness to the muffins.
- Flour – You can make this recipe using all-purpose, whole wheat, or a combination of both. I have also had luck using a good-quality all-purpose gluten-free flour mix.
- Chocolate Chips – I usually use semi-sweet chocolate chips for this recipe, but dark chocolate would be great too.
- Greek Yogurt – I like to use a plain, non-fat Greek yogurt for these muffins. It adds protein and calcium, while also giving them a nice, soft texture. Regular yogurt, or even dairy-free yogurt, can be used instead, if needed.
- Buttermilk – These muffins can be made with any milk, dairy, or non-dairy. I like to use buttermilk because it makes the muffins nice and moist.
- Optional Additions – I also like to add in a few tablespoons of ground flaxseed and protein powder. My kids can’t even tell they’re in there, but they add essential nutrients to these muffins.

How To Make Healthier Chocolate Chip Muffins
- Preheat the oven to 350 degrees F and either line a muffin tin with liners or spray it well with cooking spray. Set aside until ready to use.
- To a large mixing bowl, add the Greek yogurt, eggs, oil, buttermilk, vanilla extract, flaxseed, protein powder, coconut sugar, and pure maple syrup. Whisk everything together until thoroughly combined.
- Next, add in the flour, baking powder, baking soda, salt, and cinnamon. Use a large spoon or a spatula to mix the batter until all ingredients are well combined. Add in the chocolate chips and mix one more time.
- Divide the batter evenly into the muffin tin. I like to add a heaping 1/4 cup of batter into each spot, but you can make them as large or as small as you want. I also like to add a few extra chocolate chips to the top of each muffin, but that is optional.
- Place the muffin tin in the preheated oven and bake until the muffins are cooked through and an inserted toothpick comes out clean, about 25 minutes. Remove muffins from oven and let cool in the muffin tin for about 10 minutes, before transferring them to a cooling rack to cool completely.

Recipe Frequently Asked Questions
- Make this recipe gluten-free by using your favorite gluten-free all-purpose flour blend.
- Make this recipe vegan by using a plant-based milk and a vegan egg substitute.
- What makes this muffin recipe healthy? I like to use unrefined sugar, like coconut sugar and maple syrup. I also add ground flaxseed and protein powder. Whole wheat flour can be used, if you wish.
- How many muffins does this recipe make? This recipe makes 12 large muffins, 48 mini muffins, or one loaf.
- Are muffins freezer-friendly? Yes, these muffins can be frozen. Allow them to cool completely, then place in an air-tight, freezer-friendly container for up to 3 months.
- How long do leftover muffins last? If stored in the refrigerator, in an air-tight container, muffins should last about 5 days. They can also be stored at room temperature, but they might not last quite as long.
Have a question I didn’t answer? Ask me in the comment section below, and I will get back to you ASAP!

Looking For More Muffin Recipes?
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Healthy Apple Cinnamon Muffins
Print
Healthy Chocolate Chip Muffins
- Total Time: 40 minutes
- Yield: 12 1x
- Diet: Vegetarian
Description
These Healthier Chocolate Chip Muffins are packed with protein and nutrients. They’re the perfect, guilt-free way to satisfy your sweet tooth in the morning, and the added plant based protein will help you to feel full until your next meal. These healthy muffins can be made regular sized, mini or even in a loaf pan.
Ingredients
- 1 cup plain, non-fat Greek yogurt
- 2 large eggs
- 1/2 cup canola oil, or unflavored oil of choice
- 1/2 cup buttermilk, or milk of choice
- 1/2 cup coconut sugar
- 1/4 cup pure maple syrup
- 2 teaspoons vanilla extract
- 2 tablespoons ground flax seed
- 1-2 scoops protein powder, optional
- 2 cups all purpose flour, or whole wheat
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon cinnamon
- 1/4 teaspoon salt
- 1 cup chocolate chips, plus more for toppings muffins with, if desired
Instructions
- Pre-heat oven to 350 degrees F and either line a muffin tin with liners, or spray it well with cooking spray. Set aside until ready to use.
- To a large mixing bowl, add the greek yogurt, eggs, oil, buttermilk, vanilla extract, flax seed, protein powder, coconut sugar and pure maple syrup. Whisk everything together until completely combined.
- Next, add in the flour, baking powder, baking soda, salt and cinnamon. Use a large spoon, or spatula, to mix the batter together until all ingredients are mixed in well. Add in the chocolate chips and mix one more time.
- Divide the batter evenly into the muffin tin. I like to add a heaping 1/4 cup of batter into each spot, but you can make them as large, or as small, as you like . I also like to add a few extra chocolate chips to the top of each muffin, but that is optional.
- Place muffin tin into the pre-heated oven and bake until muffins are cooked through, and an inserted toothpick comes out clean, about 25 minutes. Remove muffins from oven and let cool in the muffin tin for about 10 minutes, before transferring them to a cooling rack to cool completely.
Notes
*Flour is measured by scooping the measuring cup into the flour and then leveling it off.
Muffins should be stored in an air-tight container, either at room temperature or in the refrigerator. They should stay fresh for about 4-5 days.
They can also be stored in the freezer for up to 3 months. Just make sure they are packed in an air-tight, freezer friendly container.
- Prep Time: 15 mins
- Cook Time: 25 mins
- Category: Breakfast, Vegetarian
- Method: Oven
- Cuisine: American


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