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Disappearing Muffins (Gluten Free, Pumpkin Chocolate Chip Oatmeal Muffins)

disappearing muffins

I cannot keep these pumpkin chocolate chip muffins in the house for more than a few days before they completely disappear. So we started calling them ✨ 🪄 Disappearing Muffins 🪄 ✨ You'll find me making a double (or even triple!) batch to freeze so I don't have to bake them so often! While these are a departure from the simple prep with minimal ingredients recipes I typically create and post, these yummy, pumpkin chocolate chip muffins are totally worth the work. They are loaded with ingredients I feel good about eating myself, and feeding my kids. They have fiber from whole rolled oats, pumpkin and chia, are relatively low in sugar thanks to coconut sugar, and have lots of essential nutrients with zero preservatives compared to store bought muffins. 

There are lots of options and variations, see the notes below. 

Makes 24 Muffins



2 cups Oats (to make 1 1/2 cups ground, or 1 1/2 cups oat flour)
1 cup All Purpose Gluten-Free Flour
1 1/3 TB Pumpkin Pie Spice
2 tsp Baking Powder (aluminum free)
1 tsp Baking Soda
1 tsp Sea Salt
1 1/2 cups Oats (whole, rolled)

15 ozs Pureed Pumpkin (1 can unsweetened)


1 cup Unsweetened Applesauce
1/2 cup Plain Whole Milk Yogurt
2/3 cup Coconut Sugar (or light brown sugar)
1 1/3 TB Vanilla Extract
2 Egg (room temperature)
1/4 cup Butter (melted)
1 cup Dark Chocolate Chips (mini chips work best)
2 TB Chia Seeds
1/3 cup Water

disppearing muffins2

(already starting to disappear!)




Preheat oven to 375 degrees F.

Line 24 standard sized muffin tins with parchment cupcake liners, or spray/brush lightly with avocado or coconut oil. Set aside.

In a small bowl, combine chia seeds and water and set aside.

Pulse 2 cups of whole rolled oats in a blender or food processor to make 1 1/2 cups of oat flour. Pour into a large mixing bowl.

To the large mixing bowl, add remaining dry ingredients, except whole oats and whisk well to fully combine.

Once all dry ingredients are evenly whisked, stir in whole oats.

In a separate, medium bowl, place pumpkin puree, apple sauce, yogurt, vanilla extract, brown sugar and chia seed mixture. Whisk well to combine.

Whisk in eggs.

Slowly drizzle in melted butter, whisking constantly to combine.

Pour wet ingredients into dry, and gently stir with a spatula to combine fully, until only a few streaks of flour remain.

Add chocolate chips, continue mixing by hand until fully incorporated and no white streaks remain.

Divide evenly between 24 muffin liners, using a scoop or spoon, filling at least 3/4 of the way up.

Bake at 375F for 20-22 minutes, or until the internal temperature reads 200 degrees F. (Do not overbake)

Cool muffins in the pan for 5 minutes, then remove to a wire rack to finish cooling.


  • Vegan

To make these vegan, substitute 1/2 cup whole milk yogurt with 1/3 cup plant based milk. Use all chia instead of any eggs: Combine 4TB chia seeds total and 10TB water total, allow to sit while you prepare dry ingredients and all other wet ingredients. Combining the wet ingredients using a high power blender will provide a smooth consistency.

  • No Chia

If you don't have chia seeds on hand, you can substitute an equal amount of ground flax seed and follow the same instructions, OR use 2 additional eggs. 

  • Mini Muffins
    If you prefer to make a mini version of these muffins, bake at 350 degrees F for 12-15 minutes, checking for doneness (springy top and 200 degree internal temp) at 12 minutes. They may be smaller, but I doubt it will help them last any longer!
  • Baking multiple trays
    If baking multiple trays at once, rotate trays top to bottom racks, and front to back about halfway through baking time to promote even cooking.
  • Storage
    If they last longer than a day, store in an airtight container on the counter for up to two days, or in the refrigerator for about 5 days (if they last that long) Microwave refrigerated muffins for 15-30 seconds for just-baked texture.
  • Freezing
    Allow muffins to cool completely, at least one hour, and place in a single layer in a freezer bag. Remove as much air as possible when sealing. Store flat in the freezer up to three months.
  • Optional Additions/Substitutions
    Replace chips with (or add) chopped nuts, seeds or chopped dried fruits up to 1 cup total addition. Any more may require adjustment of wet ingredients.

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