Bakery Style Gluten Free Chocolate Chip Muffins

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Who does not love fresh-baked bakery style gluten free chocolate chip muffins straight from the oven? These soft and fluffy muffins (with the perfect high dome and an amazing texture) are a chocolate lover's dream come true. I use Mini Chocolate Chips instead of regular chocolate chips. This way every bite has lots of chocolate and is packed with flavor. Oh, and did I mention those muffins aren't overly sweet? If you are new to gluten-free baking, this is the perfect recipe for you to start out with.

If you love muffins, make sure to check out my other gluten-free recipes for Gluten Free Lemon Poppy Seed Muffin Recipe and my Gluten Free Apple Cider Donut Muffins.

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Recipe Ingredient Notes
How to make Gluten Free Chocolate Chip Muffins
Storage & Freezing
How will I prevent the chocolate chips from sinking?
Why should I sift the dry ingredients together?
FAQ for Gluten Free Chocolate Chip Muffins
Join my Gluten Free Community!
Note about Salt in my Recipes
Baking in grams
Note about Ovens and Oven Temperatures
Substitutions and Modifications
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💬 Comments

Recipe Ingredient Notes

Gluten Free Flour: I tested this recipe for Gluten Free Chocolate Chip Muffins with Bob's Red Mill 1 - to 1 and my own DIY Gluten-Free Flour Blend. The muffins created with King Arthur came out with a dense crumb. Cup4Cup turned the batter into a very gummy mess. If you plan on using a different brand, I highly recommend one containing several different flours as well as a binder like xanthan gum.

Butter: I use unsalted butter in my recipes. Please use cold butter, straight from the fridge, for this recipe.

Milk: I have tested this recipe with whole fat and low-fat milk as well as Almond milk. All three work great here - so any milk you have in your fridge will work (do NOT use buttermilk!)

Mini Chocolate Chips: I recommend using Mini Chocolate Chips in this recipe for chocolate chip muffins. Large Chocolate Chips or chunks may sink to the bottom of the muffins and burn. If you don't have access to Mini Chocolate Chips, I recommend using regular chocolate chips and giving them a rough chop before adding them to the batter. I also top the muffins with a generous amount of chocolate chips when I remove them from the oven. Because there is no such thing as too much chocolate.

Ingredients needed to make gluten free chocolate chip muffins

How to make Gluten Free Chocolate Chip Muffins

To make these gluten-free blueberry muffins you will a standard muffin pan, a stand mixer fitted with the paddle attachment, a flexible spatula, and a medium/large cookie scooper. And of course a digital kitchen scale.

Using cold ingredients in this recipe will help the muffins rise and result in a beautiful bakery-style muffin.

Step 1: Line a standard muffin pan with 12 muffin liners and set aside. Sometimes they are called Muffin Cups or Cupcake liners.

Step 2: Start by sifting together the gluten-free flour, cornstarch, baking powder, baking soda, kosher salt, cinnamon, brown sugar, and granulated white sugar in the bowl of your stand mixer fitted with the paddle attachment.

Step 3: Cut the unsalted, cold butter into small in ½ inch cubes and add to the dry ingredients. Mix at a low speed for about 2 minutes until it resembles a very coarse consistency. Add your mini chocolate chips and mix to combine.

Step 4: In a separate bowl whisk together the cold milk, large eggs, and vanilla extract. Add the wet ingredients to your dry ingredient/butter mixture and blend together. Your batter for chocolate chip muffins will be very thick.

Step 5: Using a large cookie scoop (like this #20 scoop) fill each cup with batter all the way to the top. Top with additional chocolate chips (and coarse sugar if you like).

Place in the fridge while your oven preheats to 350F. Resting your muffin batter, even if it's just 15-30 minutes will help hydrate the flour which builds a better crumb.

At this point, you can store the chocolate chip muffin batter in your fridge for up to 3 days. I like to just go ahead and scoop them into the muffin tins and carefully cover them with foil. When I am ready to bake, I don't have to wait around and can pop them right into the preheated oven.

Step 6: Bake the gluten-free chocolate chip muffins at 350F for 18 minutes, rotate the muffin pan, and continue to bake for an additional 8 - 10 minutes until they are golden brown and feel firm. You can check with a toothpick to make sure the middle is fully baked (Insert a toothpick in the middle of your muffins - it should come out clean with no raw dough stuck to it)

Step 7: Carefully remove the muffin pan from the oven and place it on a wire rack. Allow the gluten free chocolate chip muffins to cool in the muffin pan for 5 minutes before carefully removing them to a cooling rack to cool completely. If you allow them to cool completely in the muffin tin, the heat can't escape and the muffin papers will be soggy.

Storage & Freezing

Store the gluten-free muffins in an airtight container at room temperature for up to 3 days. These muffins are best eaten the day they were baked.

To freeze the gluten-free muffins, place them on a sheet tray and pop them in the freezer for 30-45 minutes or until they are solid. Once frozen transfer them to an airtight container or freezer bag. Freeze up to 3 months. When ready to eat, allow for them to thaw at room temperature or nuke in the microwave for 15-30 seconds.

How will I prevent the chocolate chips from sinking?

Since this muffin batter is on the thicker side, you don't have to worry about your chocolate chips sinking to the bottom. If you are worried about all your chocolate chips sinking, you can always scoop one small scoop of plain muffin batter into the muffin tins before adding the chocolate chips. Please remember if you do this, you will have more chocolate chips in the "upper half" of your muffins. I use this method to make my Gluten Free Blueberry Muffins.

Why should I sift the dry ingredients together?

Sifting dry ingredients together may seem like an extra step Chefs like to add to the recipe but there is actually a reason behind the sifting. Not only does sifting dry ingredients make sure all the ingredients are blended well but it also helps to lighten up the flour mixture. You don't need a fancy kitchen tool for this. I use a strainer I have had for as long as I can remember. I place it over the bowl of my kitchen aid mixer and sift the ingredients right into my bowl.

Bakery Style Gluten Free Chocolate Chip Muffin made with Bob's Red Mill 1-1 and Mini Chocolate Chips

FAQ for Gluten Free Chocolate Chip Muffins

Can I freeze gluten free muffins?

Yes, I recommend allowing them to cool completely and then freeze on a sheet tray for 2-3hrs. Then transfer to an airtight container or ziplock bag. Thaw on the counter at room temperature. I recommend nuking them in the microwave for 15-30 seconds to melt the chocolate in the center before eating.

Can I make muffin batter ahead of time?

Yes. As a former bakery owner, I would make my muffin batter the night before and bake them in the morning. Keep this in mind for the holidays - think fresh-baked muffins on Thanksgiving or Christmas Morning. But without making a huge mess in your kitchen the second you get up. Resting the batter for several hours or even overnight gives the starches in the flour more time to absorb the moisture from the liquid ingredients used in the batter.

How long will muffin batter last?

Please use the Gluten Free Muffin Batter within 48 - 72hrs.

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Note about Salt in my Recipes

I use Diamond Kosher Crystal Salt in all of my recipes unless otherwise stated. If use use a different brand or kind of salt in your kitchen please adjust accordingly since some salts can be saltier. If you use Morton’s Kosher Salt please be aware that their salt granules are smaller in size, denser, and crunchier and twice as salty.

Baking in grams

I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and easy to use. You can purchase them on Amazon for less than a set of measuring cups. For small amounts under 10 grams, I like to use this Precision Pocket Scale. Measuring cups are very inaccurate which can cause significant errors when it comes to gluten-free baking or baking in general. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons. To learn more about Baking with a digital scale, make sure to check out my post about Baking by weight.

Note about Ovens and Oven Temperatures

All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.

If you are baking with convection (fan-forced), please adjust the recipes accordingly. Convection oven can cause baked goods to dry out quickly and still be raw inside. Since takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.

Substitutions and Modifications

Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.

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Yield: 12 regular sized or 6 gigantic muffins