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Gluten Free Little Bites Muffins

Gluten Free Little Bites (chocolate chip) Muffins

My kids used to LOVE the little bites muffins. You know the ones, the mini chocolate chip muffins packaged neatly into single serve bags. But I just couldn’t stomach the LONG LIST of ingredients! So I scoured the internet for a homemade version. When I found it, I noticed it needed a little modifying to fit our dietary needs. Below you have my tested and true version of Little Bites Muffins, and they’re gluten free! They’re best served fresh, but then I often store them in the fridge to help them last longer. These can be made in a larger muffin tin or as mini muffins. You’ll just need to adjust the baking time accordingly (larger muffins need a bit longer to bake, around 18-22 minutes depending on your oven. My oven takes even longer, 25-28 minutes but it’s a convection oven). 

These are perfect to add to school lunches, bus ride snacks, or even for breakfast combined with fruit and yogurt or milk! Give ’em a try and let me know what you think in the comment section.

Happy Baking!

Gluten Free Little Bites Muffins

Lindsey Remmers
The gluten free homemade version of the ever popular little bites chocolate chip muffins! Makes 24-30 bite-size mini muffins.
Prep Time 15 minutes
Cook Time 14 minutes
Total Time 29 minutes
Course Breakfast, Snack
Servings 24 bites

Ingredients
  

  • 1 1/2 cups gluten free flour blend 1-to-1 baking blend
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/4 tsp salt
  • 1 1/4 cups yogurt Greek or regular
  • 1/2 cup maple syrup
  • 1/3 cup unsalted butter melted and cooled
  • 2 large eggs
  • 2 tsp vanilla extract
  • 1 cup mini chocolate chips

Instructions
 

  • Preheat the oven to 375°F (190°C) and line a mini muffin tray with muffin liners OR lightly spread butter into each muffin space. Set aside.
  • In a medium bowl, whisk together the gluten free flour blend, baking powder, baking soda, and salt until well combined.
  • In a separate medium bowl, stir or whisk together the yogurt, maple syrup, eggs, melted butter, and vanilla extract until smooth and fully incorporated.
  • Gradually add the wet ingredients into the dry ingredients, mixing until just combined. Batter will be thick and sticky.
  • Gently fold in the chocolate chips, ensuring they’re evenly distributed throughout the batter.
  • Using a small spoon or ice cream scoop, fill each muffin cup in the tray, making sure not to overfill (they rise quite high!)
  • If you have leftover batter, you can fill another tray of regular size muffins or mini muffins. Be sure to add water to any unfilled muffin space (fill the muffin space about 1/3 full with water).
  • Bake for 10-12 minutes, or until the bites are golden brown and a toothpick inserted comes out clean. Extend baking time if baking 2 muffin sheets.
  • Let the mini bites cool completely before serving.

Notes

Whole wheat flour works great in this recipe too.
To ensure this recipe is Low FODMAP, use lactose-free yogurt and Enjoy Life chocolate chips.
Keyword gluten free, low fodmap, muffin

Last Updated on December 11, 2025 by Lindsey Remmers

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Hi, I’m Lindsey

I’m a Functional Dietitian with a Master’s degree in exercise science and nutrition. I’m dedicated to transforming lives through functional nutrition support targeting root causes. With LiveEatPerform Nutrition, my clients receive more than just dietary advice; they embark on a holistic wellness journey, gaining the knowledge and tools to live a life of energy, balance, and happiness.