Pumpkin Chocolate Chip Cupcakes {gluten free, low FODMAP}

Oct 18, 2019 | Dessert, Gluten free, Holidays, Recipes

It’s the day after Labor Day, and I’m walking into Whole Foods. I look up and see… pumpkins. Rows upon rows of pumpkins. It literally looks like someone picked up an entire pumpkin patch and dropped it on Whole Food’s doorstep.


My reaction: WHAT?!? No. PUMPKINS?! no. Wait! It’s still summer! NO. It’s way too early for pumpkins.


Marc’s reaction: PUMPKINS! yes! It’s… pumpkin time! We can make pumpkin pie! and pumpkin cookies! and pumpkin cake! and pumpkin bread! … and pumpkin soup! and pumpkin lattes! and…

Well apparently someone likes pumpkin.

Now don’t get me wrong: I love pumpkin season. But I’m not in any hurry to end summer too soon! (And up until just now, it still felt like summer in Texas…) So yes, I know I’m a little late onto the pumpkin bus here. Hopefully you’re not too pumpkin-ed out? Because I’ve got some super delicious pumpkiny and chocolatey pumpkin cupcakes here!



These guys are completely gluten free, but seriously, you’d never know it. I love making gluten free baked goods like these because, frankly, it’s so easy! Yes, I really did say that. Yeasted breads like rolls and pizza and such can be really difficult to make gluten free, but I think baked goods have the potential to be even better than their wheat-full counterparts. The flavors you get from all the different flours can never be achieved with regular old wheat flour.

Plus! These cupcakes are full of pumpkin and chocolate chips! And everyone knows that pumpkin + chocolate = DELICIOUSNESS. Oh, and by the way, when I call these cupcakes, I really mean I only made them cupcakes because I’m convinced that my bread pan is on a mission to ruin my life. Seriously everything I make in that thing ends up horrible. So… cupcakes for me. BUT if you’re like, so totally over cupcakes and have a benevolent bread pan, by all means make this into pumpkin bread if you want. Also, I “frosted” mine with pumpkin yogurt, but only because I COMPLETELY FORGOT about the crumble topping! But I’ve made these with the crumble before, and I do highly recommend it. Or, if you happen to have pumpkin yogurt on hand, I can now endorse that route as well. (Or if you want to make frosting, of course, do that.)


Alright, I’m done rambling. Time for ALL THE PUMPKIN!

Pumpkin Chocolate Chip Cupcakes

Yield | 9 cupcakes or one 9.5 loaf
These can be made into either cupcakes or bread.
Be sure to let these cool completely, as they will set as they cool. (Otherwise they'll fall apart.)
For the pictures, I used pumpkin greek yogurt as frosting (because I forgot the streusel) but I highly recommend the streusel topping.


  • 1 cup pumpkin puree
  • ¼ cup oil I did half melted coconut oil and half olive oil
  • 2 tablespoons butter melted
  • 2 eggs
  • 1 tablespoon maple syrup
  • 2 teaspoons vanilla extract
  • ¼ cup brewed coffee, or milk
  • ¼ cup + 2 tablespoons quinoa flour
  • ¼ cup + 2 tablespoons sticky rice flour
  • ¼ cup millet flour
  • ¼ cup oat flour
  • ¼ cup tapioca starch
  • ¾ cup brown sugar packed
  • 1 teaspoon baking soda
  • ½ teaspoon salt
  • 2 teaspoons cinnamon
  • 1 teaspoons nutmeg
  • ½ teaspoon cloves
  • ½ - ¾ cup chocolate chips


  • 2 tablespoons salted butter cold, cubed
  • ¼ cup brown sugar
  • ¼ cup oat flour
  • ¼ cup old fashioned oats
  • 1 teaspoon cinnamon
  • dash salt


  • Preheat the oven to 350 degrees F. Spray a muffin tin or 9x5 loaf pan thoroughly with nonstick spray.
  • Whisk together the pumpkin puree, oil, butter, eggs, maple syrup, vanilla, and coffee in a medium size mixing bowl until smooth.
  • In a separate bowl, combine the flours, brown sugar, baking soda, salt and spices until just combined.
  • Pour liquid mixture into dry and add the chocolate chips. If the dough seems too dry, stir in the buttermilk. Pour the mixture into the prepared pan.
  • To make the streusel, add the brown sugar, flour, oatmeal and cinnamon to a mixing bowl. Add the butter and, using your hands, work the butter into the dry ingredients until everything evenly crumbly. Sprinkle the streusel over top of the cupcakes.
  • Bake for 20 minutes or until the top is lightly golden. Remove from the oven and let sit 5-10 minutes, then invert the bread out onto a clean surface. Sprinkle with powdered sugar if desired, slice and enjoy warm with cold milk or hot coffee!

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