Bakery Style Gluten Free Keto Chocolate Chip Muffins

In the realm of baked goods, few treats rival the universal appeal of perfectly baked Bakery Style Gluten Free Keto Chocolate Chip Muffins.

These low carb gluten-free chocolate chip muffins are warm, fluffy, and bursting with chocolate chip flavor.

Muffins are a perfect go-to snack or breakfast option for the whole family, including myself, with a morning cup of coffee or glass of unsweetened almond milk.

Finding a bakery-style muffin that meets the gluten free and low carb requirements for someone who has a gluten intolerance is a daunting task so fear not, you have found the perfect gluten-free muffin recipe!

I love having these muffins ready to go when my kids want a snack, or to tide them over while breakfast gets made without worrying about spoiling their appetite as there is no sugar.

These healthy chocolate chip muffins are the perfect amount of sweetness that is not too overpowering.

Taking time out of your weekend or day off for a little gluten-free baking has allowed us to enjoy our favorite baked goods without missing out!

A great way to measure chocolate chips is with your heart because you can never have enough chocolate chips in these gluten-free muffins!

Each bite has a melty chocolate bit that goes great with the coconut flour base! 

There is no need for a gluten free all-purpose flour with this recipe, just simple ingredients that include coconut flour, sugar free maple syrup and sugar free chocolate chips! 

The best combination of ingredients for gluten free baking yield the best fluffy muffins!

I do not use any xanthan gum in this recipe as it is not needed.

The best part is that this recipe is for a small batch but it can be doubled easily without any recipe adjustments. 

You will be pleasantly surprised how these muffins will dome just like bakery-style chocolate chip muffins!

Keep reading as I take you through making this easy recipe with wholesome ingredients, as well as give tips, substitutions and answer frequently asked questions.

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Ingredients you will need to make these Gluten Free Muffins

• Coconut flour (Bob’s Red Mill is my favorite as it is good quality)
• Baking soda as the leavening agent (not baking powder as this usually has corn starch in it)
• Sea Salt
• Stevia
• Avocado oil or liquid vegetable oil like melted coconut oil or olive oil
• Large eggs, room temperature
• Heavy Cream or Coconut cream(the thick part of canned coconut milk)
• Keto Maple Syrup
• Apple Cider Vinegar
• Vanilla Extract

Let’s make some Bakery Style Gluten Free Keto Chocolate Chip Muffins

Preheat your oven to 425F and prepare your muffin tin with paper liners or greasing very well.

Baking at a higher temperature than the usual 350F lends to a higher rise without extra leavening ingredients.

I actually grease my muffin liners too with a short burst of cooking spray to make sure they come off of the paper without sticking. Set aside.

In a large bowl, add the coconut flour, baking soda, sea salt, and stevia.

Whisk all of the dry ingredients well and then set aside. 

In a medium bowl add the oil, eggs, heavy cream, maple syrup, apple cider vinegar and vanilla extract.

Whisk the wet ingredients together well until smooth.

Now add the wet ingredients to the flour mixture and whisk until smooth.

Don’t worry about over mixing the muffin batter, as coconut flour is not finicky like a gluten-free flour blend would be to extra mixing.

Now you will fold in the coconut flour dusted sugar free chocolate chips gently with a wooden spoon or rubber spatula right before scooping into the muffin liners.

Fill the muffin cups 2/3 full as this is a better way to achieve the raised and domed muffin top like bakery style muffins!

Add extra chocolate chips on the top of each well of batter and bake for 18-20 minutes until lightly golden brown on top.

I recommend checking it a few minutes before the time is up as your oven temperature may vary on how hot it is from my oven.

You can use a cake tester or toothpick to see that there are no crumbs left when poked in the center of a muffin.

Test by gently pressing the middle and if it springs back, then they are done.

Now let them cool only for a minute in the pan and immediately remove to a cooling rack. Putting them on a wire rack to cool will prevent them from continuing to cook in the pan.

My favorite part is to brush them with some melted butter while they are still hot, if you are a butter person!  You can keep these gluten free chocolate chip muffins up to 5 days on the counter in an airtight container. 

Store in the fridge up to 7 days or in the freezer for 3 months. If you are freezing, flash freeze on a baking sheet for one hour then wrap individually with plastic wrap.  After you have wrapped each one to prevent freezer burn, then transfer all wrapped muffins into a large freezer bag. 

To eat, just thaw overnight in the fridge or in the oven at 300F for 8 minutes from frozen.

Tips, Substitutions, and FAQs

• Make these gluten-free chocolate muffins when you replace 2 tablespoons of the coconut flour with 2 tablespoons of cocoa powder.
• If you run out of eggs and do not have enough needed, you can substitute 1 egg with 1/3 cup sour cream if you wish.
• You can jazz these up by adding in some sugar free peanut butter chips or white chocolate chips!
• There is no substitute for coconut flour. You can find my other recipes using almond flour if you do not have coconut flour.
• My favorite sugar free chocolate chips are dark chocolate chips! They lend a very rich flavor to these gluten free chocolate chip muffins!
• If you do not have apple cider vinegar, you can easily use lemon juice in its place without any issues.
• You could use melted unsalted butter instead of the liquid oil. It may make the muffins more cakey versus tender crumbed though.
• I have never tried an egg replacement or flax eggs in this recipe because eggs are needed for structure. Find an almond flour recipe instead or one using King Arthur gluten-free flour..
• If you want to try a different sweetener other than stevia like coconut sugar, or brown sugar, stick to using a 1/4 measuring cup at most. Remember it can also change the texture of the muffin.
• You can try replacing the oil with 1 mashed banana if you are not watching your carbs, to make gluten free banana chocolate chip muffins. You can of course leave out the chocolate chips if you want to make plain gluten-free banana muffins.

Can I double the recipe to make more than 6 muffins? ​If you double the recipe, you will need not just one 12-cup muffin pan but 2 pans since the trick to making these muffins rise up high like bakery-style muffins is to leave an empty well in-between each muffin.

​Can I use something else other than chocolate chips with this recipe? Yes, you can easily turn this into a recipe for gluten-free blueberry muffins when you add in the same number of blueberries. The base of this recipe is perfect for gluten free blueberry muffins or even cranberry or raspberry muffins. When you substitute 1/4 cup pumpkin puree for one of the eggs you can make gluten-free pumpkin muffins. 

​Can I substitute the coconut flour with almond flour or oat flour? ​No, you cannot substitute any other flour for the coconut flour. Coconut flour requires more liquid ingredients for the recipe to work out as it is a very thirsty flour. 

Is there a way to make this dairy free? Yes, it is dairy free already if you choose to use coconut milk instead of the cream. You can also try unsweetened almond milk or oat milk if you wish. This is the only ingredient that would need to be substituted as the oil is already dairy free.

Would a flax egg work or an egg replacement work for the eggs to make these vegan chocolate chip muffins? ​The eggs are a big part of the muffin having lift, as well as providing the right liquid ratio for the coconut flour. You could try it, but I am not sure of the results so it would be an experiment for you.

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If you love cast iron as much as I do, then you would absolutely LOVE my 2nd cookbook “Chaffles Cast Iron and The Crock” !!

Try my other recipes using sugar free chocolate chips!

Easy Gluten Free Low Carb Carmelita Bars Recipe

Keto Healthy Double Chocolate Muffins

Seven Layer Magic Bars Recipe (Keto and Dairy Free)

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