Low-FODMAP ‘Copycat’ Panera Chocolate Chip Muffies (Muffin Tops); Gluten-free, Dairy-free

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My son’s favorite thing to have at Panera is a chocolate chip muffie. So he was very disappointed when the Panera near our house stopped selling them.  Why would they do that?

Not to be deterred, I decided to create a ‘Copycat’ Panera low-FODMAP Chocolate Chip Muffie.  Plus, that way I could also enjoy them.  Best idea ever!

A muffie aka a muffin-top is the very best part of a muffin!  More like a cake than a muffin (in my opinion), it has all the benefit of the chewy caramelized edges, and moist, fluffy insides.

This low-FODMAP ‘Copycat’ Panera Chocolate Chip Muffie is super easy and so delicious.  I opted to buy a muffin top pan to help me make it, but I think the pan will come in handy for egg, buns, and other recipes anyway.

Try this low-FODMAP ‘Copycat’ Panera Chocolate Chip Muffie with chocolate chips, or swap for blueberries, nuts or other stir-ins.  It is so yummy you won’t believe it is safe for the low-FODMAP diet.

You may also love my low-FODMAP Copycat Starbucks Iced Lemon loaf and low-FODMAP Chocolate Chip cookie  recipes. Or check out out over 300 more low-FODMAP recipes on the blog.  IBS-friendly!

Be healthy and happy,

Rachel Pauls, MD

Low-FODMAP ‘Copycat’ Panera Chocolate Chip Muffies (Muffin Tops); Gluten-free, Dairy-free

Although this recipe has not been tested, a single serving should be low-FODMAP based on the ingredients.

Serves: about 14 muffies / muffin tops, depending on their size

Prep time: 15 minutes

Bake time 13-18 min (*as ovens vary, begin checking about 2-3 minutes prior to end time)

Total time: 30 minutes

Bake 350 F

Equipment: 1-2 muffin top pans (I used Norpro Puffy Muffin Top Pan 4″ Wide .5″ Deep); I own one pan and did three separate bake rounds to bake all the batter


  • 2 cups low-FODMAP, gluten-free flour (I use Authentic Foods GF Classical Blend- the results are so consistent!  Check out my low-FODMAP bake off blog to see why)
  • 1 cup granulated sugar
  • 1 tablespoon baking powder
  • 1 teaspoon baking soda
  • 3/4 teaspoon xanthan gum; if not added to your flour choice
  • 1/4 teaspoon salt
  • 7 tbsp low-FODMAP milk (almond milk for dairy-free version or lactose-free)
  • 1/2 cup canola oil
  • 2 large eggs, room temperature
  • 2 teaspoons vanilla extract
  • 1 & 1/2 cups mini semi-sweet chocolate chips
    • Enjoy Life brand makes vegan mini chocolate chips
    • This will make the low-FODMAP muffies very chip-dense.  For a lighter amount of chips try 1 & 1/4 cups instead
  • Vegetable shortening or baking spray, for greasing


  • Preheat oven to 350 F and place rack in center of oven (if you are using two racks to fit the trays in your oven, then alternate trays midway through baking)
  • Grease muffin top tins with vegetable shortening or spray
  • Mix low-FODMAP flour, sugar, baking powder, baking soda, xanthan gum in large bowl
  • In another medium bowl or large measuring cup, whisk together the 7 tablespoons low-FODMAP milk and 1/2 cup oil
  • Add eggs and vanilla to milk/oil mixture and whisk again
  • Place the liquids into the flour mixture and stir until just combined by hand, or with electric mixer
  • Fold in chocolate chips by hand, batter will be somewhat sticky
  • Scoop about 1/4 cup low-FODMAP muffin top batter into individual tins (I used a large cookie scoop, this was the perfect size for 14 muffin tops)
  • Bake about 13-18 minutes, they will be light golden and puffed in the center
    • My oven took 15 min for 1/4 cup size scoops
  • Allow to sit about 5 minutes then transfer to a rack to cool
  • These freeze beautifully…my batch lasted a few weeks because I rationed them out for weekends only 😉

While they don’t look ‘exactly’ like a Panera chocolate chip muffie, the taste of these low-FODMAP Copycat Panera chocolate chip muffin tops is bang on.  So soft, moist and delicious!  My son is beyond thrilled.

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  1. Anonymous July 6, 2022
    • Rachel Pauls Food July 6, 2022

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