Mini Chocolate Chip Muffins

Tender mini muffins made with whole grain flour, Greek yogurt and mini dark chocolate chips.

Mini muffins in a basket

Sometimes we just want a little morsel or bite of something sweet or a fun little snack which is why I’m such a fan of mini food, whether that be energy balls, squares of dark chocolate or these mini chocolate chip muffins.

They’re perfect to pack in lunches, for a grab and go snack or to serve with breakfast or brunch.

The other cool thing is I’ve made the recipe a bit healthier than the traditional chocolate chip muffin, but they have the best flavor and texture, so we’re getting the best of both worlds with these little guys!

How to make mini chocolate chip muffins

These muffins have some pretty standard ingredients: flour, baking powder, salt, sugar, oil, eggs, vanilla and milk. I also added yogurt for a spongier product and a bit more protein (definitely try it!).

These muffins are mini, meaning they are made in a mini 24-cup muffin tin. If you don’t have one, here is one my favorites: Wilson Premium Non-Stick Mini Muffin and Cupcake Pan (affiliate link).

If want to make them in a 12-cup muffin tin, you totally can! They will just take a bit longer to cook; I’d start checking on them at 15 minutes.

My tip for making tender, flavorful muffins

Sometimes muffins can turn out tough, chewy or flavorless, so I have a few tips for making the best, most tender and delicious muffins!

Don’t overmix the batter. I realize this is incredibly subjective, but if you simply mix the dry ingredients and wet ingredients separately, then mix the two together until just mixed, you’ll be good to go!

I generally avoid using a hand or stand mixer to make muffin batter because it’s easy to overmix. I use a whisk to mix together the dry ingredients, then the wet ingredients, then I use a spatula to fold the ingredients together to make the batter.

I also almost always use mix-ins like chocolate chips or blueberries in my muffins, so be careful to fold those in gently as well, and only until they are incorporated. The mix-ins will help add flavor to the muffins, but I like the actual batter to have great flavor as well, and that’s where extracts come in.

When it comes to batter flavor, most people think of vanilla extract right away, and I do too – I LOVE vanilla extract and always put extra in my baked goods. But I also love almond extract, and in this particular recipe, the flavor lends itself really well. I put it as optional in the recipe, but I HIGHLY recommend it.

You can also add a crumble to the top of your muffins to make them extra delicious!

Mini muffins in a basket

Tips for making muffins healthier

When I’m developing muffin and other baked good recipes, there are a few tricks I usually use to make them a bit healthier. Baking is a science, so it’s important not to make so many changes to the recipe that it doesn’t turn out or resemble the taste, texture and appearance of the original.

A few of my favorite ways to lighten up baked goods and make them a bit nutritious include:

  • Swapping out about half of the flour for whole wheat pastry flour (whole wheat is fine, too). Swapping out half will up the fiber content, but doesn’t usually change the texture of the final product. I am also a big fan of using rolled oats or oat flour (ground oats) in my recipes because oats are super great for you!
  • Using Greek yogurt as the “liquid” to bring the batter together (sometimes the batter also requires milk). I love using yogurt because it gives a nice fluffy texture to the batter and also provides quite a bit of protein. Baked goods usually don’t have much protein, so this is a bonus!
  • Adding ground flax seed to boost the omega 3s and fiber. If it’s just a few tablespoons, you can usually just add it without changing the recipe. But if you’d like to use more, you can swap out a little bit of the flour for ground flax. Sometimes I use almond flour in my baked good recipes as well, but it’s not really a good idea to completely swap in almond flour, as it generally requires changes to other ingredients (change in liquid ratio, more eggs, etc.).
  • Adding nuts and/or fruit. Both are super nutritious and add amazing flavor and texture to baked goods. Go crazy here!
  • Cutting down on the sugar – generally cutting down by about half of the original recipe won’t change the texture and the recipe will still turn out. I generally cut the original amount in half and test that out first, then make changes if needed. If you use sweeteners like maple syrup or honey the texture and taste will change some, and sometimes for the better! I use all types of sugar in my baked goods depending on the flavor I’m going for (for example, I love brown sugar with cinnamon). When you first cut back on sugar in your baked goods, it can seem like they’re not sweet enough, but once you get used to it, you’ll find traditional baked goods are far too sweet.
Mini muffin in a hand

Can these muffins go in the freezer?

And last tip, but not least, is these little morsels of muffin goodness can go in the freezer! That is, if you don’t eat them all right away. Let them fully cool, then toss them in an airtight container or Ziploc freezer bag and get them in the freezer.

They will last 1-2 months and you can grab them out one at a time or go for multiples! They’re perfect for lunch boxes, as a grab and go snack or to compliment a high protein breakfast. Regardless, these chocolate chip mini muffins are SO GOOD!


Mini Chocolate Chip Muffins

Mini muffins in a basket

Mini muffins made with whole grain, Greek yogurt and mini dark chocolate chips.

  • Author: Julie Andrews
  • Prep Time: 5-10 mins
  • Cook Time: 10-15 mins
  • Total Time: 15-25 mins
  • Yield: Makes 24 mini muffins 1x
  • Category: Snacks, Breakfast
  • Method: Baking
  • Cuisine: American


  • ½ cup whole wheat or whole wheat pastry flour
  • ½ cup all-purpose flour
  • 1 teaspoon baking powder
  • ¼ teaspoon coarse salt
  • ⅓ cup granulated sugar
  • ¼ cup oil
  • 1 large egg
  • 1 ½ teaspoons pure vanilla extract
  • ¼ teaspoon pure almond extract (optional)
  • ¼ cup plain or vanilla Greek yogurt
  • ¼ cup milk
  • ¼ cup mini dark or semisweet chocolate chips


  1. Preheat the oven to 350 degrees. Line a 24-cup mini muffin tin with mini muffin liners. Set aside.
  2. In a medium mixing bowl, whisk together the flours, baking powder and salt until combined. In a separate medium mixing bowl, whisk together the sugar, oil and egg vigorously until mixture is fluffy and pale. Whisk in the vanilla extract, almond extract (if using), yogurt and milk until incorporated.
  3. Pour wet ingredients into the bowl with the dry ingredients and fold until just incorporated. Fold in the chocolate chips.
  4. Use two spoons to scoop mixture into mini muffin tin wells. Bake 9-13 minutes or until just set. Let cool before serving.


Cooking Tip: Don’t overmix the muffin batter. Mix only until all ingredients are incorporated.


  • Serving Size: 1 mini muffin
  • Calories: 73
  • Sugar: 4g
  • Sodium: 41mg
  • Fat: 3g
  • Saturated Fat: 1g
  • Unsaturated Fat: 2g
  • Trans Fat: 0g
  • Carbohydrates: 9g
  • Fiber: 1g
  • Protein: 1g
  • Cholesterol: 8mg

Keywords: muffin, muffins, mini muffins, chocolate chip, baked goods

Did you make this recipe?

Did you make this recipe? Share a photo and tag us on Instagram and Facebook @thegourmetRD. We can’t wait to see your creation!

You might also like...

Join the Discussion

Leave a Comment

Your email address will not be published. Required fields are marked *

Recipe rating

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Scroll to Top