clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon
Gluten-Free Pumpkin Muffins Recipe

Gluten-Free Pumpkin Muffins Recipe with Cream Cheese & Chocolate Chips

  • Author: Rebecca Baron
  • Prep Time: 20 minutes
  • Cook Time: 20 minutes
  • Total Time: 40 minutes
  • Yield: 14 1x
  • Category: Breakfast
  • Cuisine: Gluten-Free


I made jumbo, bakery style muffins but regular would obviously work the same (and I wrote the recipe for regular sized muffins). I thought the jumbo would be fun for the pictures, though. I thought these were the best muffins I've ever had.




  • 1 ¾ Cups Quinoa Flour *
  • 2 Tbl Tapioca Flour *
  • 1 ½ tsp Baking Powder
  • ½ tsp Baking Soda
  • ½ tsp Real Salt *
  • ¾ Cup Gluten-Free Old Fashioned Rolled Oats
  • 2/3 Cup Brown Sugar (packed)
  • 2 Eggs
  • ¾ Cup Pumpkin Puree
  • ½ Cup Apple Sauce
  • 1 tsp Vanilla
  • ¼ Cup Milk
  • ½ Cup Mini Chocolate Chips (or nuts, if desired)


  • 6 oz Cream Cheese (softened, 3/4 pkg.)
  • 2 drops Cinnamon essential oil
  • ¼ Cup Powdered Sugar


  • ½ Cup Brown Sugar
  • ¼ Cup Gluten-Free Old Fashioned Rolled Oats
  • 2 Tbl Quinoa Flour *
  • ¼ tsp Cinnamon
  • 1 ½ Tbl Butter


  1. Preheat the oven to 350 degrees. Grease or line a muffin tin with baking wrappers.
  2. In a large bowl, whisk together the quinoa flour, tapioca starch, baking powder, baking soda, salt, and oats.
  3. In another mixing bowl, whisk together the brown sugar, eggs, pumpkin puree, apple sauce, vanilla and milk until smooth.
  4. Mix the wet ingredients with the dry ingredients until just combined.
  5. Add the chocolate chips and mix in until distributed. Set aside.
  6. In another bowl, beat the softened cream cheese, cinnamon oil, and powdered sugar together until smooth and creamy. Set aside.
  7. In another bowl, mix together the brown sugar, oats, quinoa flour and cinnamon. Cut the butter in with your fingers until it resembles fine crumbs.

To assemble muffins:

  1. Fill each muffin well(about 14) ½ way with pumpkin muffin batter. Divide the cream cheese mixture between the muffins, placing on top of the batter. Divide the remaining muffin batter between the muffin wells, placing over the top of the cream cheese.
  2. Sprinkle the streusel topping over evenly over the top of the muffins.
  3. Bake in the preheated oven for 18-20 minutes, or until puffed and firm on top.
  4. Let cool completely before eating.

Keywords: Rich, Decadent, Bakery Style