
These bakery style chocolate chip muffins bring the coffee shop experience right to your kitchen with their perfect dome tops and melty chocolate chips in every bite. I developed this gluten-free version after my daughter was diagnosed with celiac disease, determined to make treats that everyone would enjoy regardless of dietary restrictions.
This recipe became our Sunday morning tradition when my daughter felt left out at birthday parties. Now our neighbors request these muffins more than any other treat I make.
Ingredients
- Gluten free flour: With xanthan gum creates the perfect texture without any grittiness
- Cornstarch and water mixture: Acts as an egg substitute while ensuring a tender crumb
- Milk: Provides moisture and helps activate the leavening agents
- Vegetable oil: Keeps these muffins moist for days longer than butter would
- Vanilla extract: Enhances the chocolate flavor without overpowering
- Semi sweet chocolate chips: Offer the perfect balance of sweetness look for high quality chips that melt well
Step-by-Step Instructions
- Prepare Your Equipment:
- Preheat oven to 375°F and thoroughly grease a jumbo 6-cup muffin tin including the top surface. This prevents sticking when the muffins rise above the cups creating that coveted bakery style dome.
- Mix Dry Ingredients:
- Combine gluten free flour, sugar, baking powder, baking soda, and salt in a large bowl with a whisk. The thorough mixing here ensures the leavening agents are evenly distributed leading to consistent rising.
- Create Wet Mixture:
- Mix cornstarch and water until completely smooth and watery. This creates a binding agent similar to eggs. Add milk, oil and vanilla, whisking until fully combined for a homogeneous liquid mixture.
- Combine Mixtures:
- Slowly incorporate wet ingredients into dry ingredients using a gentle hand. Switch to a spatula when the batter thickens to avoid overworking the gluten free flour which can make muffins tough.
- Add Chocolate Chips:
- Fold in 1.5 cups of chocolate chips with a spatula using a gentle motion that maintains air bubbles in the batter. This step creates pockets of melty chocolate throughout each muffin.
- Fill Muffin Cups:
- Use an ice cream scoop to portion batter evenly to the top of each cup. Smooth the tops gently with the back of a spoon to ensure even baking and that classic domed appearance.
- Add Topping:
- Sprinkle remaining chocolate chips on top of each muffin and press lightly to adhere. This creates an appetizing appearance and ensures chocolate in every bite including the crispy top.
- Bake to Perfection:
- Bake on the center rack for exactly 29 minutes until golden and springy. The precise temperature and timing creates the iconic bakery style dome without drying out the interior.

The cornstarch mixture is my secret weapon in this recipe. I discovered it by accident when I ran out of eggs one morning and was desperate to keep our Sunday tradition alive. The resulting texture was actually better than my original version, creating an incredibly tender crumb that stays moist for days.
Storage Tips
These muffins maintain their texture best when stored in an airtight container with a paper towel on the bottom to absorb excess moisture. For longer storage, wrap each cooled muffin individually in plastic wrap and place in a freezer bag for up to three months. Thaw at room temperature or microwave for 20 seconds for that fresh baked taste.
Making Them Non-Gluten Free
If you don't need gluten free muffins, simply substitute regular all purpose flour for the gluten free flour. Reduce the amount to 1¾ cups even without the additional 2 tablespoons as regular flour absorbs moisture differently than gluten free varieties. The cornstarch mixture still works beautifully as an egg substitute even with regular flour.
Flavor Variations
Transform these muffins with simple additions while keeping the base recipe intact. For double chocolate muffins, add 3 tablespoons of cocoa powder to the dry ingredients. Create chocolate orange muffins by adding the zest of one orange to the wet ingredients. For chocolate chip banana muffins, reduce milk to 1 cup and add ⅓ cup mashed ripe banana to the wet mixture.

Frequently Asked Questions
- → Can I use regular flour instead of gluten-free flour?
Yes, you can substitute regular all-purpose flour in equal amounts. Since the recipe calls for gluten-free flour with xanthan gum, you won't need to add any additional binding agents when using regular flour.
- → What does the cornstarch and water mixture do in this recipe?
The cornstarch mixture acts as an egg substitute while also helping to create a tender crumb structure. It provides binding properties and contributes to the muffins' fluffy, bakery-like texture.
- → Can I make these as regular-sized muffins instead of jumbo?
Absolutely! For standard-sized muffins, fill the cups to the top as directed, but reduce the baking time to approximately 18-22 minutes. Check for doneness when the tops are golden and spring back when lightly touched.
- → How should I store these chocolate chip muffins?
Store completely cooled muffins in an airtight container at room temperature for up to 3 days. For longer storage, freeze them individually wrapped in plastic and placed in a freezer bag for up to 3 months.
- → What can I use instead of vegetable oil?
Melted coconut oil, canola oil, or melted butter can be substituted for vegetable oil. Each will impart a slightly different flavor profile, with butter offering a richer taste.
- → Why are my muffin tops not domed like bakery muffins?
For higher domed tops, make sure your oven is fully preheated to 375°F before baking. Also, filling the muffin cups completely to the top and starting with a higher temperature (425°F) for the first 5 minutes before reducing to 375°F can help create that bakery-style dome.