These mini chocolate chip muffins are absolutely adorable and incredibly tasty, making them the ideal bite-sized treat for kids and adults alike! Soft, fluffy, and loaded with chocolate chips in every bite, they’re sweetened just right and made with wholesome ingredients like Greek yogurt and a touch of whole wheat flour for added nutrition without compromising the flavor.
Growing up in the Midwest, I learned that the best treats are the ones made with love in your own kitchen, using simple ingredients that you can feel good about serving your family. I’ve been passionate about making muffins and quick breads for more than 20 years, and they’ve become one of my favorite ways to fill our kitchen with the warm, comforting aromas of home baking. My daughter especially loves helping me make muffins, and there’s something so special about watching her carefully measure ingredients, help mix the batter together, and eagerly wait by the oven for them to finish baking.
I specifically developed this recipe after my daughter asked (okay, whined!) about why we never buy those packaged mini chocolate chip muffins at the store. Instead of giving in to processed snacks full of preservatives, I challenged myself to create a homemade version that would be even more delicious and nutritious. After several test batches and plenty of taste-testing from my eager family, I landed on this recipe that combines the convenience and fun of mini muffins with wholesome ingredients that make them suitable for lunchboxes, after-school snacks, or even as a little sweet treat with your weekend brunch spread.
Why You’ll Love These Mini Chocolate Chip Muffins
Kid-approved taste. All the sweetness and chocolate chip goodness kids crave, but made with better-for-you ingredients that you feel good about sharing with your family.
Hidden nutrition. Greek yogurt and whole wheat flour add protein and fiber without affecting the taste.
Mini size. Bite-sized muffins are fun for little hands to hold, and a small treat for kiddos to enjoy! Let’s be honest, adults love a quick, small bite too.
Great for breakfast, lunchboxes, and snacking! Grab for an on-the-go breakfast or as a little sweet side to eggs. Pack them as a yummy lunchbox treat, or surprise your little friends with these as a special after school snack.
Ingredients for Our Greek Yogurt Chocolate Chip Muffins
- Large egg. Provides structure and helps bind all the ingredients together while also adding richness to the muffins.
- Vegetable or canola oil. Keeps the muffins moist and tender without making them heavy.
- Vanilla extract. Enhances the overall flavor and complements the chocolate chips beautifully.
- Vanilla Greek yogurt. Adds protein, moisture, and a subtle tang while keeping the muffins incredibly soft and fluffy.
- Milk. Helps create the right batter consistency and adds additional moisture.
- Granulated sugar. Provides sweetness and helps create the light, tender texture.
- Salt. Enhances all the other flavors and balances out the sweetness.
- Baking powder. The leavening agent used to help our muffins rise and become fluffy.
- All-purpose flour. Forms the base structure of the muffins and provides the classic muffin texture.
- Whole wheat flour. Adds nutrition, fiber. Used in combination with all-purpose flour to ensure the muffins aren’t too dense or heavy.
- Mini chocolate chips. Provides bursts of chocolate in every bite! Mini chocolate chips are just the right size for mini muffins.
Helpful Equipment
You’ll need mini muffin tins (a 24-cup capacity one works well for this recipe, or just use 2, 12-cup mini muffin tins). I also love using a small cookie scoop for evenly portioning out the batter.
Muffin Size
Dividing your batter between 22 muffin cups gives you a little bit bigger mini muffins whereas dividing the batter between 24 muffin cups gives you more of the ‘little bites’ sized muffins (you know, those pre-packaged ones that we’re replacing with this much more delicious recipe!).
How to Make Mini Chocolate Chip Muffins
Prep the muffin tins. Fill 22-24 mini muffin cups with mini liners or grease with non-stick baking spray, wiping off the top of the pan to prevent burning.
Mix together the wet ingredients. In a large mixing bowl, whisk together egg, oil, vanilla extract, vanilla Greek yogurt, and milk until well combined.
Add in the granulated sugar and whisk to combine with the wet ingredients.
Slowly add in the dry ingredients. Start by adding the baking powder, baking soda, and salt.
Then slowly mix in the flours until about 75% combined. You should still see some streaks of flour at this point.
Add the chocolate chips. Gently fold in the mini chocolate chips until JUST combined. A few lumps are okay, do NOT don’t overmix!
Rest the batter and preheat the oven. Allow the batter to rest for about 10 minutes. This step helps the muffins to rise the best, but skip it if you don’t have time. While the batter rests, preheat the oven to 350°F.
Fill the muffin cups. Evenly distribute the batter between the prepared muffin cups, filling each about ⅔ full (I like to use a small cookie scoop to do this).
Optional: add a few extra chocolate chips on top for a bakery-style look and extra chocolate goodness.
Bake. Place the filled muffin tin(s) on the oven’s middle rack and bake until a toothpick inserted in the center comes out clean (about for 9-14 minutes).
Cool. Let the baked mini muffins cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely.
How Long to Bake Mini Muffins
Mini muffins bake much faster than regular-sized muffins due to their smaller size. Bake for 9-14 minutes at 350°F, checking with a toothpick after the 9 or 10 minute mark to avoid overbaking. The tops should be lightly golden and spring back when gently touched.
Mini Chocolate Chip Whole Wheat Muffins Variation Ideas
- Different mix-ins. Swap the mini chocolate chips for wild blueberries (they’re little too!), other mini baking chips, or chopped nuts.
- Yogurt swaps. Swap out the Vanilla Greek yogurt with an equal amount of sour cream, regular yogurt (vanilla or plain), or even applesauce. You may need to reduce the amount of milk used when doing this for the right batter consistency (start with 1 Tablespoon instead of 2 and add more as needed).
- Make them vegan. Substitute the egg with a flax egg, and use plant-based milk and yogurt. Please note that I have not done this, but this should work just fine based on common baking swaps.
Expert Tips for Baking Mini Muffins
Don’t overmix the batter! This makes a huge difference when baking any type of muffin. Mix until the ingredients are JUST combined (a few lumps are ok!) to avoid tough, dense muffins.
Use mini chocolate chips. Regular sized chocolate chips are too large and heavy for mini muffins.
Fill cups evenly. Having your muffins the same size ensures they’ll bake at the same rate. I like to use a small cookie scoop to help me portion out my muffin batter.
Test for doneness early. Mini muffins can go from done to overbaked quickly. So check your muffins with a toothpick at the start of the baking range (around the 9 or 10-minute mark).
Cool completely before storing to prevent condensation which can lead to soggy bottoms.
Serving Suggestions for Chocolate Chip Muffins
- Enjoy with a savory breakfast: Serve alongside your favorite egg dish for a little pop of sweetness to round out the meal. We love these alongside our egg bites and some oven cooked bacon!
- Breakfast on the go: Pack 2-3 mini muffins with fresh fruit for an easy and balanced morning meal.
- Lunchbox treats: These fit perfectly in all kinds of lunch containers, are a fun bite-sized treat, and are less messy than full-size muffins.
- After school snacks: Pair with a glass of milk for a satisfying afternoon treat.
- Add to your brunch spread: Arrange on a tiered stand or platter for a sweet and easy options for brunch parties.
How to Store Mini Chocolate Chip Muffins
Store fully cooled muffins in an airtight container at room temperature for up to 3 days. For longer storage, keep them in the refrigerator for up to one week, though they’re best enjoyed within the first few days.
To help maintain freshness, you can also place a paper towel in the bottom of the container to absorb any excess moisture. If muffins seem a bit dry after storage, warm them in the microwave for 10-15 seconds.
How to Freeze and Thaw Mini Chocolate Chip Muffins
To freeze: Place completely cooled muffins in a freezer-safe container or bag, separating layers with parchment paper. They’ll keep for up to 3 months in the freezer.
To thaw: Remove the desired number of mini muffins from the freezer and let them thaw at room temperature for 30-45 minutes. For quicker thawing, simply microwave frozen muffins for 20-30 seconds, checking every 10 seconds to avoid overheating.
Chocolate Chip Mini Muffins Recipe FAQs
While you can use regular chocolate chips, mini chips work much better in mini muffins. Regular chips are heavier and can sink to the bottom or make the muffins uneven. If you only have regular chips, I’d recommend roughly chopping them into smaller pieces first.
The most common cause is overmixing the batter. Once you add the flour, you want to mix until you JUST can’t see dry ingredients. This is why we recommend adding the chocolate chips when you’re about 75% stirred together. A few lumps are completely normal and ok for muffins. Overmixing develops the gluten too much, creating tough muffins.
Yes, you can substitute the Greek yogurt with an equal amount of sour cream, regular yogurt, or even applesauce. You may need to reduce the amount of milk used when doing this for the right batter consistency (I’d recommend starting with 1 Tablespoon of milk instead of 2 Tablespoons and adding more as needed). Keep in mind that Greek yogurt provides extra protein and tanginess, so the flavor and nutrition will be slightly different.
Either use mini paper liners in each muffin cup or thoroughly grease the each muffin cup with non-stick spray. If using spray, make sure to wipe off any excess from the top of the pan to prevent burning. Let the muffins cool for 5 minutes before removing to help them release more easily.
Yes, you can definitely make these into bigger, standard-sized muffins! Since our base recipes makes about 22-24 mini muffins, you’ll end up with 11-12 regular sized muffins.
To make regular sized muffins, simply grease or line a standard sized muffin tin and fill the muffin cups about ⅔ full with batter. Regular-sized muffins typically bake for 18-25 minutes, so begin checking for doneness around the 18 minute mark using the toothpick test (insert a toothpick into the center of a muffin. It’s done when the toothpick comes out clean or with just a few moist crumbs, not coated in wet batter).
Love This Recipe? Try One of These Easy Muffin Recipes Next!
Greek Yogurt Chocolate Chip Muffins
Equipment
- Small Cookie Scoop (optional, but helpful for portioning out the batter)
Ingredients
- 1 large egg
- ½ Cup vanilla Greek yogurt (we like the 2% vanilla bean from Cabot)
- ¼ Cup neutral oil (vegetable or canola)
- 2 Tabelspoons milk of choice (we use 2% dairy milk)
- ½ teaspoon vanilla extract
- ⅓ Cup granulated sugar
- ¾ teaspoon baking powder
- ¼ teaspoon baking soda
- ¼ teaspoon salt
- ½ Cup all-purpose flour
- ½ Cup whole wheat flour
- ½ Cup mini chocolate chips + more for topping if desired
Instructions
- Prep. Preheat the oven to 350°F. Fill 22-24 mini muffin cups with mini liners or grease the cups with non-stick baking spray (wiping off the top of the pan to prevent burning).
- Mix together the wet ingredients. In a large mixing bowl, whisk together the egg, yogurt, oil, milk, and vanilla extract. Then whisk in the granulated sugar.1 large egg½ Cup vanilla Greek yogurt¼ Cup neutral oil2 Tabelspoons milk of choice½ teaspoon vanilla extract⅓ Cup granulated sugar
- Slowly mix-in the dry ingredients, starting with the baking powder, baking soda, and salt. Mix until about 75% combined (you’ll still see streaks of flour at this point).¾ teaspoon baking powder¼ teaspoon baking soda¼ teaspoon salt½ Cup all-purpose flour½ Cup whole wheat flour
- Add in the chocolate chips. Gently fold in the mini chocolate chips until JUST combined (a few lumps are ok! Do NOT overmix).½ Cup mini chocolate chips + more for topping if desired
- Rest the batter. Allow the batter to rest for about 10-minutes (skip if you don’t have time, but this helps the muffins rise best).
- Transfer the batter to the prepared muffin cups. Fill the muffin cups evenly (about ⅔ full) – I like to use a small cookie scoop to do this. Sprinkle a few extra mini chocolate chips on top of each muffin if desired.
- Bake on the oven's middle rack until a toothpick comes out clean (about 9-14 minutes). Start checking on the early side of the time window to help prevent overbaking / drying them out.
- Cool. Let the mini muffins cool in the pan for about 5 minutes and then transfer them to a wire rack to cool completely.
Kristin says
My kids loved these!! They really do taste like the little bites mini muffins, but better!!
Meredith says
So happy to hear your kiddos love these too!!
Courtney says
These are my kids favorite school snack and mine too! So easy to make and they are super yummy!!!
Meredith says
YAY!! I’m so glad you all love these mini muffins too Courtney 🙂
Lynn says
My kids loved these! They are perfect for after school snacks and for a quick breakfast!
Meredith says
I’m so happy to hear the kids loved these Lynn! Thanks for giving our recipe a try 🙂
David says
It’s taking all my willpower not to eat, idk, 7 of these at a time. So good!
Meredith says
I totally get it, they’re so yummy and easy to grab *just one more*… 😉
Alison Narveson says
When I saw you trialing these I was so excited for the recipe to come. My oldest kiddo is gf so we tried it with a measure for measure flour and they turned out fabulous! The entire crew loved them. Another batch will be needed asap.
Meredith says
I’m so happy the whole crew loved them! And glad to know cup for cup GF flour worked wonderfully. Thanks for making these Alison!
Meredith says
My kiddo has DEVOURED every single batch of these we’ve made. Great to add into their lunchbox too!