Healthy Pumpkin Apple Crisp {gluten free}

Pumpkin Desserts & Baked Goods

Pumpkin and apples comes together with warm fall spices in every bite of this delicious gluten free pumpkin apple crisp! It’s the perfect treat to make if you’ve got a surplus of freshly picked apples and love all things pumpkin!

If you’re asking yourself what to do with all of those apples from a weekend spent apple and pumpkin picking, this healthy pumpkin apple crisp is truly the perfect thing! Made gluten free with simple ingredients and a lot of love for the season, this crisp is sure to be a fall treat you’ll want to make again and again.

We just got back from apple picking in Michigan at am apple orchard and pumpkin patch that we go to every year. The kind that still has the pumpkins on the vine in the field and apples you can pick right off the branch. It was a beautiful, crisp autumn day and I was feeling all of the fall vibes!

We picked northern spy, empire and red delicious apples and I frolicked in the pumpkin patch with my dog, Pumpkin!

To top it all off, I had one of the best apple cider donuts ever, which inspired me to make something with apples and pumpkin that was a little bit on the healthier side. This healthy, and gluten free pumpkin apple crisp!

healthy pumpkin apple crisp

Pumpkin and apples are quintessential fall, and I just love pairing the two together like I did here in this pumpkin apple baked oatmeal. This time I wanted a crisp with big baked apple chunks and a crumbly pumpkin seed oat topping! I kept the skin on the apples for more fiber per bite!

I mixed pumpkin puree into the apple mixture and it baked together so perfectly, almost like I covered the apples in pumpkin butter. I used gluten free flour from Trader Joe’s, plus oats, pumpkin seeds, all of the fall spices, and gluten free granola for this crumble that will have you coming back for seconds!

Top it with ice cream, pumpkin spice whipped cream or my favorite, siggi’s pumpkin spice yogurt and a drizzle of melty peanut butter!

how to make a healthy pumpkin apple crisp

Ingredients for Healthy Pumpkin Apple Crisp

  • apples (I used empire, northern spy and a honeycrisp)
  • pumpkin puree
  • pumpkin seeds
  • butter
  • gluten free flour
  • coconut sugar
  • cinnamon
  • nutmeg
  • pumpkin pie spice
healthy gluten free pumpkin apple crisp

Healthy Pumpkin Apple Crisp {gluten free}

Maggie Michalczyk, RDN
This pumpkin apple crisp embodies what fall is all about. It will make your entire house smell delicious as it bakes and is perfect for any fall occasion! 
Prep Time 10 minutes
Cook Time 45 minutes
Servings 10 servings


  • Filling:
  • 4-5 medium-large apples some tart (like granny smith or northern spy, some sweet (like honeycrisp)
  • 1 lemon juiced
  • 1/2 tsp. lemon zest grated
  • 1/3 cup pumpkin puree
  • 1/2 cup coconut sugar or sub organic cane sugar
  • 1 1/2 tsp ground cinnamon
  • 3 tbsp arrowroot starch or cornstarch for thickening
  • 3/4 tsp fresh grated ginger
  • 1 pinch nutmeg
  • Topping:
  • 1 cup gluten-free rolled oats*
  • 1/2 cup gluten-free flour*
  • 1/2 cup 1 stick grass-fed butter, melted and cooled ***
  • 1/3 cup pumpkin seeds pepitas
  • 1/4 cup coconut sugar or sub brown sugar
  • 1/4 cup pecans roughly chopped
  • 1/4 tsp sea salt
  • 1 tsp. pumpkin pie spice
  • 1 tsp ground cinnamon
  • gluten-free granola I love this pumpkin one from Purely Elizabeth!


  • Preheat oven to 350 degrees F.
  • Wash and thinly slice apples lengthwise (keep the skin on for extra fiber!)
  • Add to a large mixing bowl and top with remaining filling ingredients. Toss to combine.
  • Add apple and pumpkin mixture to a 9×13 baking dish.
  • In another small bowl add all topping ingredients. Stir to combine, then use fingers to break down any clumps of sugar. Pour over apples in an even layer.
  • Bake for 45-50 minutes (uncovered) or until the filling is bubbly, and the apples are very fork tender.
  • Top with extra gluten free granola if desired and serve with ice cream or pumpkin spice greek yogurt. 
  • Keep the leftovers covered in the refrigerator up to 3 days. Reheat in the microwave. 


* If gluten is not as issue, feel free to use regular oats and whole-wheat or whole-wheat pastry flour 
*** Cool butter in a hurry by microwaving a glass of water, until warm/hot, dumping the water out and placing the cup over the butter. 

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