Baked Apples Stuffed with Spiced Butternut Squash and Gingersnap Crumble

By Amanda Paa – Updated April 8, 2023

The way I see it, fall should really be called baking season. There’s no other time of the year that compares in terms of all the delicious, in-season eats that can be turned into comforting desserts. Warm apple crisp, creamy pumpkin pie, spice cookies ….. it’s hard to choose which to make first.

I said yes to all of them this year by making these caramelized baked apples, stuffed with silky, spiced butternut squash. To give them the crunch and spice that fall sweets deserve, Annie’s Gluten-Free Gingersnap Cookies were the perfect finishing touch. And could their bunny be any cuter?

Baked Apples Stuffed with Spiced Butternut Squash & Gingersnap CrumbleMost years, the apple tree in the backyard of my childhood house would be so full that we couldn’t even give them all away. Besides her famous apple pie, my mom would often bake them, stuffed with brown sugar and oats. I liked this treat, but like any child, I would have always voted for the more decadent pie. Now that I’m older, I appreciate these “mature” desserts much more. It satisfies a weeknight craving for something warm and sweet, and makes a very special breakfast too.

You’ll want to start with crisp apples like ones that you would use for pie or a cobbler. I used Sweet Sixteen’s, but Haroldson or Honeycrisp would be great too. Some recipes keep the apple whole and dig out the center core for your filling, but cutting them in half (with some of the inner apple removed) and adding them to a cast iron skillet is the secret to caramelized, cinnamon infused edges.

how to make stuffed apples

For the filling, I couldn’t turn my back on squash and for good reason. Not that you couldn’t make pumpkin work, but squash has less water content and therefore makes a stiffer puree, holding its shape perfectly when you pipe it into the apples. Plus the roasted squash (which you can do at the same time the apples are baking) has a sweeter, nuttier flavor that pumpkin from a can doesn’t have. If you were to use pumpkin, you would need to add a thickener like full fat greek  yogurt or cream cheese to ensure it doesn’t collapse.

Baked Apples Stuffed with Spiced Butternut Squash | heartbeet kitchen

I love using Annie’s products beyond just snacking because they’re such an easy way to adapt recipes that may traditionally have gluten. The gluten-free gingersnaps are perfect for things like this crumble or what I often use in recipes to replace graham cracker crumbs. Most importantly I can feel good about eating their snacks because Annie’s is dedicated to using real ingredients. And that bunny? Their founder made him the official “rabbit of approval,” representing the simplicity, care, and goodness of the products. Love it.

Baked Apples with Spiced Butternut Squash Filling

Baked Apples Stuffed with Spiced Butternut Squash & a Gingersnap Crumble

serves 6

for squash:
3 1/2 cups cubed butternut squash (a medium sized squash)
2 tablespoons olive oil
1/4 teaspoon ground nutmeg
1/4 teaspoon salt
2 tablespoons maple syrup
2 to 3 tablespoons water

for apples:
3 large apples, cut in half
2 tablespoons butter
1/2 teaspoon cinnamon
2 tablespoons packed brown sugar
2 whole cinnamon sticks
1 cup Annie’s gluten-free Gingersnap Bunny Cookies, crushed

Preheat oven to 375 degrees. Toss squash with olive oil, nutmeg and salt. Spread onto a large baking sheet. Roast for 25-30 minutes, stirring squash until it can be easily pierced with a fork and is soft.

Meanwhile, prepare apples by removing the seeds and creating a hole about 1 inch deep in the middle of each half with a melon baller. Add butter to a 1o inch cast iron skillet (or heavy baking dish) and place it in the oven for about 1 minute to melt it. Remove and stir in cinnamon, brown sugar and cinnamon sticks. Place apples cut side down in the skillet so they are not touching. Move the squash if not quite cooked through to the bottom rack and put the skillet on the middle rack of the oven. Bake for 12-15 minutes, until apples are softened, but not completely mushy. (You want them to still be able to stand up when you flip them over.) Remove apples and squash from the oven when both are done. Using a spatula, flip apples up to stop them from cooking.

Add squash to a food processor or blender with the maple syrup and process until smooth, adding a few tablespoons of water if necessary. Pipe squash into holes of the apple with a decorating gun or just spooning it in. Finish with crushed gingersnap cookies and drizzle some of the juices left in the cast iron skillet over the top. Can be made one day ahead of time (without the crumble added to the top), just reheat it warm oven for 7 minutes, then add topping.

#spon: Thanks to Annie’s for sponsoring this post! I’m required to disclose a relationship between my blog and Annie’s Homegrown. This could include Annie’s providing me w/ content, product, access or other forms of payment.

Did you make this?

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September 29, 2014


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  1. Robin Hamilton @Wellness Wires

    I prefer healthy food! And I’ll definitely try these baked apples stuffed with spiced quash and gingersnap crumble. My husband would love it! Thanks and kudos for this awesome recipe.

  2. Bella Hardy

    Wow! this is gorgeous. I bet Baked Apples Stuffed with Spiced Butternut Squash and Gingersnap Crumble would be scrumptious amazing for kids. Will definitely try this for my son.

  3. Jill Roberts @ WellnessGeeky

    I finally got to make these baked apples stuffed spiceds quash gingersnap crumble this past weekend and it was such a hit!! I’m also gonna pin this post on my Pinterest board my followers will love it. Thanks for sharing, Amanda!

    • amandapaa

      I’m so glad you liked the recipe, Jill! xo

  4. Sunnymay

    I’ve used Annie’s Gluten Free Mac N Cheese which is made with rice instead of wheat, yet tastes good and light. By adding veggies, it becomes more colorful and a meal in one pot.

  5. Jolene

    My boyfriend and I are just getting started eliminating wheat from our diet (He seems to have some reactions to it that add to a skin condition, I just don’t want to buy/cook two meals!) So having a few snacks to reach for and know they will fit our needs is great.

  6. kathy

    Found you after listening to you on mpr! Your recipes look delicious…I look forward to reading through your blog. I’ve never used any gf annies products, just the regular, and never thought about using them in recipes. Yum.

    • Amanda Paa

      oh so glad you were able to catch the MPR talk about winter squash! and thanks for stopping by the blog. the gf annies products have been great, looking forward to trying their organic gf mac and cheese too.

  7. Jess

    Love the combination! This looks like the perfect after meal dessert!

  8. jennifer s.

    The white shells mac’n cheese, is the best ever!!!! I actually never thought to use the gf products in cooking or baking. I bet the snickerdoodles would make an awesome crust for cheese cake or pumpkin pie.

    • Amanda Paa

      i love to add spinach to the white shells mac’n cheese to get some greens in. you should definitely try using the gf cookies for a cheesecake crust, they work great!

  9. Jessica @ A Kitchen Addiction

    Love the butternut squash apple combination! This looks so good!

  10. Val

    This looks!!!! FABULOUS! you are amazing!

    • Amanda Paa

      You’re so sweet Val – hope apples are in season for you right now in Puerto Rico! xp

  11. Diane (Created by Diane)

    I love baked apples and this looks fantastic!!

  12. Sylvie | Gourmande in the Kitchen

    What a wonderful way to fill baked apples, all those flavors sound really lovely together!

  13. Erin @ Dinners, Dishes, and Desserts

    These are such a fun twist. I love the crumble too!

  14. Sharana @ Living THe Sweet Life Blog

    Hahaha I adore the idea of coining this season, baking season – it’s so true!! This recipe sounds like fall perfection ~ yummm!

  15. Gerry @ Foodness Gracious

    tHESE are so cool, I love them :)

    • Amanda Paa

      thanks for stopping by Gerry! happy fall :)

  16. thelittleloaf

    I always used to hate baked apples as a child but I’m slowly coming round to them. These look delicious and I love the idea of stuffing them – such a gorgeous, warming breakfast.

  17. Brittany @ Barr & Table

    I love crumbling the graham bunnies into yogurt :)

    • Amanda Paa

      me too, especially Siggi’s vanilla bean yogurt. thanks for stopping by!

  18. Christie - Food Done Light

    I love that you used the whole apple. It is going to be so good with the squash and gingersnap crumble.

    • Amanda Paa

      thanks Christie! apples deserve all the love this fall.

  19. Amanda @ Cookie Named Desire

    I love Annie’s! I’ve used their products for years. It’s my go-to when I want something delicious and healthy for my daughter. This looks absolutely fantastic!

  20. Marly

    When I looked at the first picture I thought it was a cinnamon roll! This might be the best way to eat an apple…ever! ;)

    • Amanda Paa

      :) so much to love about apple season – thanks for stopping by Marly!

  21. Ksenia @ At the Immigrant's Table

    I love stuffed baked apples as a rule, and these look great (they always take me back to my grandmother’s kitchen, who would simply sprinkle hers with brown sugar, walnuts and cinnamon… and it was incredible). I think Annie’s gluten-free gingersnaps make a great base for key lime and lemon bars.

    • Amanda Paa

      oh, yes – the gf gingersnaps for a lemon bar crust would be amazing I bet! thanks for stopping by Ksenia :)

  22. Melissa from

    I have a apple harvest party coming up and I think I will be making this… looks amazing!

  23. Kelli

    The Annie’s Mac and Cheese makes a perfect 1st dinner (after school snack) for my high school age son. Growing boys still love mac and cheese.

    • Amanda Paa

      ah, love it Kelli! And such an easy, wholesome thing to have on one hand.

  24. Tammy

    Everything looks good enough for company.

  25. Nathania

    I love using the crackers as a on the go snack. Sometimes we dip it in peanut butter.
    N.snaer at gmail dot com