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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2 Responses

  1. I love this recipe but they always melt once in the oven, what can I do to prevent this? They are also usually very liquid-like when I make them.

    1. Hi there,
      We aren’t sure what you mean, the chocolate chips melt? or the muffies?
      We have not had any issues with their consistency and would consider looking at your flour choice if nothing else from the recipe is unchanged. Sorry you have this issue!!

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