Holy chocolate, these Gluten Free Chocolate Chip Muffins are SO good. Okay, that was pretty lame... but I promise you these muffins are not.
A tender, moist crumb. Mini chocolate chips are perfectly distributed in every bite. It's basically like eating a chocolate chip cookie in a tender muffin form (and for breakfast - or dessert, no one's judging). What's not to love?
Seriously, this kind of tastes like a more grown-up version of Little Bites - and that makes me so happy.
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What makes these Gluten Free Chocolate Chip Muffins taste so good?
- Light brown sugar helps give these muffins their classic "cookie-like" taste.
- Greek yogurt adds necessary healthy fats and moisture to balance out the texture of the muffin.
- Vanilla extract is a must in every baked good, in my not-so-humble opinion.
- Quality chocolate chips give these muffins their decadent taste and also make it guilt-free! I prefer to use Enjoy Life chocolate chips because I can trust that they're free of corn and gluten. I order mine from Thrive Market for a little bit of savings on a 4 pack. (Get 40% off your first order + sometimes a free gift.)
- Melted butter also helps give these muffins their "cookie-like" taste.
- Organic milk because if it's not organic, I don't use it. Feel free to use regular milk or a non-dairy milk, such as almond. Note: I have not tested this recipe with non-dairy yogurt.

How to Make Gluten Free Chocolate Chip Muffins:
- Preheat oven to 350 F.
- Use a silicone cupcake tray or grease/place paper cups in a standard cupcake tray.
- Combine dry ingredients: gluten-free all-purpose flour, light brown sugar, baking soda, baking powder, and salt. Mix until well combined.
- Add eggs, Greek yogurt, melted butter, milk, and vanilla extract. Using an electric mixer, beat until incorporated. Tip: Do not over-mix. Fold in chocolate chips.
- Scoop batter into prepared cupcake tray until cups are ⅔ of the way full. Bake until the center is set and lightly browned on top, about 20-25 minutes. Tip: All ovens are different and baking varies depending on altitude and humidity, please keep an eye on your muffins while baking so they don't overcook.
- Allow muffins to cool in pan for 5-10 minutes. Transfer to a wire rack to cool completely before storing.
- Enjoy.

What is the Best Way to Store Muffins?
Muffins are a quick bread, which has lots of moisture. Unlike most breads that become dry as they age, muffins actually become moister with each day that passes. If you don't store muffins properly, they can become soggy-bottomed.
The first most important step to storing muffins is: Let. Them. Cool. All. The. Way. Before. Storing. Them.
Don't become impatient, folks. Place your muffins on a wire rack, grab one to eat, and then walk away. Don't come back for a good hour, please. Then, as long as they're completely cool to the touch, you can put them away. Anxious about leaving your baked goods unattended? I'm the same way - I will literally sit at my kitchen island and read or work until time's up. It's kind of fun.
I've found the best way to store muffins is by placing them in an airtight container lined with paper towels. Place several paper towels at the bottom of the container for the muffins to sit on and then cover the tops with paper towels. The paper towels will absorb any moisture the muffins produce. While I always recommend eating quick breads within 2-3 days, you may switch out the paper towels for fresh if they become moist before then.

Tips for Baking Gluten Free:
- All gluten-free flours are different. I always recommend using a quality rice-based all-purpose flour that contains xanthum gum. Be sure your GF flour blend doesn't contain any strange ingredients that wouldn't typically be in a dessert. Watch out for flours that contain things like chickpea (or garbanzo bean) flour, pea protein, lentil flour, etc. In this recipe, I used Great Value's GF All-Purpose, which is my current go-to. It works and tastes just as well as my other trusted brands for a fraction of the cost. Other brands I recommend are: King Arthur Flour GF All Purpose flour and Bob's Red Mill 1:1 (NOT their all purpose, which contains chickpea flour).
- To measure your flour, do not scoop the measuring cup into the flour. Always use the spoon-and-level method to be sure you aren't measuring more flour than called for. Do this by simply using a spoon to scoop the flour into the measuring cup and then level off the excess with the back of a butter knife.


Gluten Free Chocolate Chip Muffins
Ingredients
- 2 cups high quality GF All-Purpose Flour with xantham gum (I used Great Value's GF All Purpose Flour)
- ¾ cup light brown sugar packed
- ½ teaspoon baking soda
- 1 teaspoon baking powder
- ½ teaspoon salt
- 2 large eggs
- 1 stick butter melted
- 1 cup plain Greek yogurt
- ¼ cup organic milk (+ 2 tbsp) (total milk = ¼ cup + 2 tbsp)
- 1 teaspoon pure vanilla extract
- 1 cup mini chocolate chips
Instructions
- Preheat oven to 350 F. Use a silicone cupcake tray or grease/place paper cups in a standard cupcake tray.
- In a large mixing bowl or bowl of a stand mixer, combine dry ingredients: flour, light brown sugar, baking soda, baking powder, and salt. Mix until well-incorporated.
- Add in eggs, Greek yogurt, melted butter, milk, and vanilla extract. Beat until just combined. Fold in chocolate chips.
- Scoop batter into prepared cupcake tray until cups are ⅔ of the way full. Bake until center is set and lightly browned on top, about 20-25 minutes. Tip: Since ovens and environments vary, keep an eye on your muffins as they bake so they don't overcook.
- Allow muffins to cool in pan 5-10 minutes before placing onto a wire rack. Allow muffins to cool completely before storing inside of an air-tight container lined with paper towels. Enjoy within 2-3 days.
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