Chocolate Chip Muffins
These chocolate chip muffins are fluffy with amazing flavor! This muffin recipe is fully loaded with chocolate chips and easy to make by hand.
Posted by Kathryne Taylor on August 26, 2025
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These chocolate chip muffins are divineโtheyโre fluffy, tender and studded throughout with chocolate chips. Theyโre our three-year-old daughterโs current favorite muffin in my muffin repertoire, and I understand why! She loves dark chocolate as much as I do, so I can vouch that these muffins delight kids and adults alike.
These muffins follow the same formula as my other popular โhealthyโ muffin recipes, but you wonโt guess it upon your first (or last) bite. Theyโre made with whole wheat flour if you wish, and theyโre sweetened with honey instead of plain sugar, which makes them extra delicious. Greek yogurt offers a subtle sour cream-like tang that makes these taste like bakery-style muffins, while providing some extra protein.
If youโre a fan of my popular banana muffins or blueberry muffins, you must try this recipe!
Chocolate Chip Muffin Tips
Do not overmix.
Your muffins will turn out tough instead of tender if you overmix this batter once the liquid is combined with the flour. Gently stir the batter together by hand, following the cues provided within the recipe, such as โyou should still see a few streaks of flour and lumps.โ If youโre unsure, err on the side of caution.
Coat the chocolate chips in cinnamon to prevent them from sinking.
This is a new trick to me, and it works brilliantly. Stirring ground cinnamon into the chocolate chips before folding them into the batter makes a world of difference, and it works better than tossing them in flour. The cinnamon flavor is lovely and subtle, and produces muffins with an even dispersion of full-sized chocolate chips throughout.
These muffins taste best after they have cooled.
I know we all love a gooey chocolate chip, but this holds true for all baked goods, especially these muffins. After resting, the flavors of coconut oil, honey, Greek yogurt and cinnamon meld and mellow, producing a truly magical muffin.
Watch How to Make Chocolate Chip Muffins
Ingredient Notes & Options
Youโll find the full recipe below. Here are my notes in case youโd like to adjust this recipe to suit your pantry or preferences.
Flour: I prefer to use whole-grain flours whenever possible for the extra fiber and flavor. These muffins turned out beautifully with whole wheat pastry flour, which has unfortunately become challenging to find in recent months. White whole wheat flour offers all the benefits of whole wheat flour without the โwheatyโ flavor. All-purpose flour will yield bakery-style muffins. Itโs up to you.
Greek yogurt: I tested this recipe primarily with whole-milk Greek yogurt, which is thick and rich, and helps support the weight of the chocolate chips. Lighter Greek yogurts will work. I wouldnโt use regular plain yogurt because it likely will not offer enough structure.
Chocolate chips: I love dark chocolate, so I enjoyed these muffins with darker chocolate chips (with a 60 percent cacao content or higher). The recipe calls for 1 cup of chips, but you can get by with 3/4 cup if need be. You can also substitute other flavored chips, such as white chocolate or buttermilk, or use coated chocolate candies like M&Mโs for more color.ย
Honey: Use regular, runny honey for this recipe. I also tried this recipe with maple syrup, which works well enough, but I preferred the flavor and greater sweetness that honey offers.
Coconut oil vs. olive oil: This is a toss-up, as far as Iโm concerned. Virgin coconut oil offers an almost imperceptible coconut flavor, whereas refined coconut oil is virtually flavorless. If you use olive oil and donโt want the muffins to taste like it, use a mild oil such as California Olive Ranch. Vegetable oil and avocado oil are also suitable alternatives.
Turbinado sugar: Sprinkling the tops of the muffins with turbinado sugar (also called raw sugar) yields a lovely little crunch, but itโs optional.
More Muffins to Make
If you enjoy these muffins, be sure to check out these muffin recipes:
- Healthy Apple Muffins
- Healthy Blueberry Muffins
- Maple-Sweetened Banana Muffins
- Healthy Pumpkin Muffins
- Healthy Zucchini Muffins
Please let me know how your chocolate chip muffins turn out in the comments! I love hearing from you.
Chocolate Chip Muffins
These chocolate chip muffins are fluffy with amazing flavor! This muffin recipe is fully loaded with chocolate chips and easy to make by hand. Recipe yields 1 dozen muffins.
Ingredients
- 1 ยพ cups (215 grams) whole wheat pastry flour or white whole wheat flour or regular whole wheat flour or all-purpose flour
- 1 teaspoon baking powder
- ยฝ teaspoon baking soda
- ยฝ teaspoon fine salt
- โ cup melted coconut oil or extra-virgin olive oil
- ยฝ cup runny honey
- 2 eggs, preferably at room temperature
- 1 cup plain Greek yogurt*
- 2 teaspoons vanilla extract
- 1 cup chocolate chips (I love semi-sweet to dark chips)
- 1 teaspoon ground cinnamonย
- Optional: 1 tablespoon turbinado sugar (also called raw sugar), for sprinkling on top
Instructions
- Preheat the oven to 375 degrees Fahrenheit. Line the muffin cups with liners or grease them with butter, coconut oil or cooking spray.
- In a large mixing bowl, combine the flour, baking powder, baking soda, and salt. Whisk them together.
- In a medium mixing bowl, combine the oil and honey and beat them together with a whisk. Add the eggs and beat well, then add the yogurt and vanilla. Mix well. (If the coconut oil solidifies upon contact with the cold ingredients, gently warm the mixture in the microwave in 30-second bursts.)
- Pour the wet ingredients into the dry and mix with a big spoon until mostly combined (you should still see a few streaks of flour and lumps).ย
- In a small bowl, stir the chocolate chips and cinnamon together (this prevents the chips from sinking to the bottom). Gently fold them into the batter (do not overmix, or your muffins will be tough).ย
- Divide the batter evenly between the 12 muffin cups (they will be pretty full, which is fine). Sprinkle the tops of the muffins with turbinado sugar, if using. Bake the muffins for 16 to 18 minutes, or until they are golden on top and a toothpick inserted into a muffin comes out clean, with no crumbs (streaks of chocolate are ok).
- Place the muffin tin on a cooling rack to cool. If you have leftover muffins, store them, covered, at room temperature for up to 3 days or in the refrigerator for up to 5 days. Freeze leftover muffins for up to 3 months.
Notes
Recipe adapted from myย Healthy Blueberry Muffins.
Nutrition
The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionistโs advice. See our full nutrition disclosure here.
Would this recipe work with mini muffins?
Hi Maura, yes, but you will just need to adjust the baking time. I would start by reducing it by half, then checking them with a toothpick.
Kate, could you use oat flour instead.
Thank you. Yvette
Hi Yvette, I find that oat flour is best in pancakes and waffles, but I have some tips for substituting with it in other recipes.
Hi Kate, cooked these choc chip muffins, absolutely delicious and healthy ingredients too.
I also made your blueberry muffins, again so delicious.
Do you have a recipe for lemon drizzle muffins.
I make the cake for hubby, but I would rather use healthy ingredients,
Regards
Barbara
Hi Barbara, I havenโt developed a lemon drizzle muffins. The closest would be my lemon raspberry muffins.
Hey Kate! This recipe looks greatโฆcanโt wait to try it. HOWEVER, my wife hates cinnamonโฆwants nothing whatsoever to do with it. Is there anything else to mix the chocolate chips with to keep them from sinking? (And by the way, why does this keep them from sinking?)โ
Thanks for all you do! You are feeding the nationโฆ
Hi Paul, if you canโt use cinnamon, you can coat in flour. In my experience the cinnamon works better, likely to do with the lighter weight. You can still get a good result with the recipe using flour instead.
Hi, Kate, I always enjoy your recipes! Thank you!
Just made the chocolate chip muffins for the first time, using the King Arthurโs Golden Wheat flour (which they say is their โrenamedโ White Whole Wheat flour). I also used whole milk Greek yogurt. The flavor and texture of the muffins are really good, but the they are a bit on the dry side, both in taste and in appearance (compared with your photo). I measured carefully and followed all directions. What did I do wrong? Perhaps the flour was lacking in moisture, or for the next batch maybe I need to add more yogurt? Or how about a ripe banana?
Hello, Iโm stumped as to why these wouldnโt have turned out with that flour and whole milk Greek yogurt. Does your oven run a little hot or did you bake for a little too long? I havenโt tried these with banana, and in all my testing the specified amount of yogurt made the muffins turn out perfectly.
I came here with the same comment. Thanks for the reply โ I will try again!!
Can I cook them in my Ninja Double Stack Airfryer?
Hi Josephine, I havenโt tested that, but if the airfryer has instructions for muffins, it should work.
These are really delicious. They are easy to make and store. Will definitely make again.
These turned out great! Iโll definitely be making them again.
Oh my, these are truly amazing! I made mini muffins with mini semisweet chocolate chips this evening to take for the first day of the school year for our preschool kids and parents tomorrow morning. I know they will go quickly. I was unable to find white whole wheat flour, so used regular whole wheat and it works well. 9 minutes cooking time was just right. Thanks for another great recipe!
Can I make these with almond flour?
Hi Cheryl, I havenโt tested these with almond flour (but I have been testing an amazing almond flour cookie I hope to share soon!). You can often substitute almond flour for regular flour, but itโs not a direct 1:1 swap due to almond flourโs higher fat content and lack of gluten. A common starting point is using less almond flour than all-purpose flour, such as 3/4 to 1 cup of almond flour for every 1 cup of wheat flour. Other adjustments may include reducing liquid or a slightly lower baking temperature.
I love these! I used Bobs 1-1 GF flour, EVOO and plain (non-Greek) yogurt and they were absolutely delicious. Youโd never know they were gluten free. Your muffin recipes are my favorite!
I made these last weekend and they were so delicious. I accidentally did a bit less sweetener (and did a mix of honey and maple syrup since I ran out of honey) and I loved how it was sweet, but also let the greek yogurt shine through.
May I pprint a print a copy of the recipe? I cannot bake from my computer,
Hello, yes feel free to print. There is a โprintโ button and you can choose the size of font and whether or not to include pictures.
Hi. I made this after trying the whole wheat blueberry muffins and loving them both. My chocolate chip muffins are sinking in the middle as they cool. Why does this happen?
Hi Purna, stirring ground cinnamon into the chocolate chips before folding them into the batter makes a world of difference, and it works better than tossing them in flour. The cinnamon flavor is lovely and subtle, and produces muffins with an even dispersion of full-sized chocolate chips throughout. You can also reserve a few and sprinkle them on top after filling the muffin cups., too.
THANKS FOR SENDING YOUR RECIPE , I LEARNED SO MUCH FROM YOU.
I LOVED BAKINGโฆ..