This healthy apple pie with whole wheat crust has all of the spicy, sweet flavors of regular apple pie, but is made with a whole grain crust and sweetened with honey. Cinnamon, ginger, honey and vanilla complement the firm, but sweet Honeycrisp apples. A healthier dessert that will satisfy that sweet tooth!

Table of Contents
Healthier Apple Pie
If you’re a lover of delicious apple pie, but are looking for a healthier version, you’ll love this healthy apple pie with whole wheat crust!
Instead of a classic double crust apple pie, this one-crust version adds a buttery, crumbly streusel topping on top. That crunchy topping makes it feel like part pie and part apple crisp – a match made in heaven!
This twist on a Dutch apple pie has the perfect balance of texture and flavor, and you’ll love serving this classic dessert during the holiday season!
For more fall-inspired desserts, you’ll also want to try this No Bake Apple Crumble and Healthy Sweet Potato Bars!

Why We Love This Whole Wheat Apple Pie Recipe
- Easy: Once your pie dough is ready, the apple filling comes together so fast. You’ll be able to enjoy a slice of your homemade pie so much quicker than you’d expect!
- From scratch: This homemade apple pie is completely homemade from the crust to the super easy apple pie filling. It’s the type of old-fashioned, home-baked dessert you’ll dream of all winter long!
- Healthier version: By using whole wheat flour instead of white flour and a healthy apple pie filling, you can enjoy the classic flavors of traditional apple pie while making it a little bit healthier. It’s still something to be enjoyed occasionally, but it will be more filling and won’t spike your blood sugar as much.
Ingredient Notes

For the crust
- Whole wheat pastry flour: This pastry flour is higher in fiber yet still has a delicate enough structure to get you the perfect flaky whole wheat crust.
- Salted butter: It’s vital to use very cold butter to get the right texture.
- Honey: This is a great alternative to regular white sugar and adds a lovely flavor to the crust.
- White vinegar or vodka: These can help keep the gluten from getting overworked so your crust doesn’t get too tough.
- Vanilla extract: Vanilla extract adds a little flavor and a delicious aroma.
- Ice water: This will hydrate the dough while keeping the butter perfectly cold.
For the filling
- Apples: Choose tart varieties like Honeycrisp or Granny Smith apples.
- Honey: This is to sweeten the filling. You can use maple syrup instead.
- Spices: Stick with classic apple pie seasonings like cinnamon, ginger, nutmeg, and salt.
- Whole wheat pastry flour: You need just a bit to help the apple filling gel in the oven.
For the streusel
- Whole wheat pastry flour
- Honey
- Salted butter: The butter will help bind the streusel filling together and give it a crunchy cookie texture.
- Cinnamon
- Salt
- Egg: Feel free to add an optional egg wash around the edge of the bottom crust for a shiny appearance and crunchy texture.
How to Make Apple Pie with Whole Wheat Crust – Step-by-Step
Make the Crust




- In the work bowl of a food processor: Pulse flour and salt three times. Add cubed butter to the flour mixture and pulse until the butter is pea size. Add in the vanilla, honey and vinegar or vodka and pulse 3 times. With the food processor running on low speed, slowly stream in ice water a tablespoon at a time, just until a dough ball begins to form.
- Place on plastic wrap and bring together into a ball, pushing with the heel of your hand if needed. Wrap with plastic wrap and form into a roughly round disc. Chill at least 30 minutes.
Make the Filling

- Preheat oven to 425℉. In a large bowl, toss apple slices with flour, salt and spices, and honey and gently toss until evenly coated.
Make the Streusel Topping

- Make the streusel topping by putting all of the ingredients into the food processor and pulsing just until it looks like wet sand and clumps together.
To assemble




- Working on a large piece of floured parchment paper, roll out the larger portion of dough for the crust with a floured rolling pin, ensuring the dough is rolled out large enough to have at least a ½ inch overhang when fitted into the pie plate, flouring as needed to prevent sticking. Place into a 9-inch pie plate, using the parchment to help lift the crust.
- Evenly pour the apple mixture into the crust, and press down lightly. Trim the excess dough from the pan and crimp the edges. Top evenly with the streusel topping.
- Place pie on a baking sheet to catch any drips. For an extra shiny crust, use a pastry brush to brush egg wash around the crust edge, being careful to not get any on the pie plate.
- Bake in preheated oven for 25 minutes. Reduce heat to 350℉ and bake for another 40 – 50 minutes, until the crust is golden brown and juices bubble up through the steam vents. If the crust starts getting too brown after the first 25 minutes, cover the crust with a pie protector or foil. Let cool completely before cutting.
Keep scrolling to the recipe card below for the full printable recipe!
Tips for the Best Healthy Apple Pie Recipe
- Tips to ensure a flaky crust: Keep all ingredients as cold as possible. I will even float ice cubes in my water to keep it ice cold. Handle the dough as little as possible. Using the plastic wrap to bring the dough together helps to keep the dough cold and reduces the chances of over handling the dough. Patting it out into a thin disk before refrigerating the dough will make rolling it out later much easier than if you were to refrigerate the dough in a ball.
- If the dough becomes too soft while working with it, put it back in the fridge to chill.
- To make the crust without a food processor: In a medium mixing bowl, whisk together the flour and salt. Place the mixing bowl with the flour into the freezer while you get everything else together. Cut the butter into the flour using a pastry blender. Add the vanilla extract, honey and vinegar or vodka, and mix quickly. Add water slowly, a tablespoon at a time, mixing with hands until no powdery flour remains. Continue with next step.
- This crust recipe doubles well for a double crust pie.
- Pecans or walnuts (chopped) can be added to the streusel topping for extra crunch.
- If you don’t want to make your own crust, this filling recipe will also work perfectly with a store bought crust.
- For a deep dish pie: Use 3 pounds Honeycrisp, 1 Granny Smith, and 4 tablespoons flour.

Recipe FAQs
This recipe uses honeycrisp and granny smith for a mix of sweet-tart flavors and textures. You want apples that will keep their shape when cooked. Pink lady, gala or jonagold are good apples for baking. Avoid red delicious and mcintosh, as they will not hold their shape and turn into applesauce.
I used Bob’s Red Mill whole wheat pastry flour for this recipe to keep the crust light and flaky, you could substitute regular whole wheat flour, or white whole wheat flour. This will give your crust a heartier texture and a darker color.
Absolutely! Apple pie typically freezes really well. It’s best to freeze the entire pie then wrap it several times in aluminum foil or plastic wrap. You can also freeze individual slices and wrap those if you want to be able to sneak a piece from the freezer here and there. The frozen pie will last well for approximately 3-4 months.
Since butter is so essential to get the perfect pie crust texture, it’s important to find a butter alternative that melts in the same way. A lot of traditional pie crust recipes call for lard. You can also try butter-flavored shortening for a vegan option.
Storage Guidelines
Leftovers are best stored in the refrigerator, tightly wrapped for up to 4 days. Leftover pie can also be stored tightly wrapped on the counter for no more than 2 days.

What to Serve with Apple Pie
There are so many ways to serve this healthy apple dessert! Serve it warm or at room temperature with vanilla ice cream or whipped cream! You may also enjoy serving this pie with a drizzle of Greek yogurt.
Try whipped coconut cream or non-dairy vanilla bean ice cream for a dairy-free topping.
It’s also lovely with a mug of Apple Spiced Tea or a Dairy-Free Pumpkin Spice Latte!
Recipe Variations
- Change the spices: You can substitute apple pie spice for the spices, or try adding cardamom, allspice, clove or orange zest for different spice notes.
- Cheddar crust: This is an unusual twist on apple pie that’s popular in the US Midwest. Add 2-3 oz of shredded cheddar cheese to the crust for a slightly salty, savory flavor that pairs well with the sweet apple filling.
- Mini apple pies: Instead of a regular pie, use mini pie pans to bake small sharing pies for 1-2 people. You may need to make extra crust or filling to accommodate the pans. Be sure to reduce the baking time as needed.


More Healthy Apple Recipes
- Healthy Apple Oatmeal Bake
- How to Make Apple Crisp Without Oats
- Healthy Apple Nachos
- No-Bake Apple Pie Cups
- Gluten-Free Apple Cinnamon Muffins
Did you make this recipe? Scroll down to leave a star rating and review!

Healthy Apple Pie with Whole Wheat Crust
Ingredients
For the crust
- 1 1/2 cups whole wheat pastry flour spooned, levelled and cold
- 1/2 teaspoon salt
- 8 tablespoons salted butter cubed and cold
- 1 tablespoon honey
- 1 teaspoon white vinegar or vodka
- 1/2 teaspoon vanilla extract
- 1/4 cup ice water
For the filling
- 2 pounds honey crisp apples peeled and sliced thinly
- 1 Granny Smith apple peeled and sliced thinly
- 1/3 cup honey
- 2 teaspoons cinnamon
- 1/4 teaspoon ground ginger
- 1/8 teaspoon nutmeg
- 1/2 teaspoon salt
- 3 tablespoons whole wheat pastry flour
For the streusel
- 2/3 cup whole wheat pastry flour
- 2 tablespoons honey
- 3 tablespoons salted butter
- 1/2 teaspoon cinnamon
- Pinch of salt
- 1 egg beaten (optional for egg wash)
Instructions
Make the crust
- In the work bowl of a food processor: Pulse flour and salt three times. Add cubed butter and pulse until the butter is pea size. Add in the vanilla, honey and vinegar or vodka and pulse 3 times.
- With the food processor running on low speed, slowly stream in ice water a tablespoon at a time, just until a dough ball begins to form.
- Place on plastic wrap and bring together into a ball, pushing with the heel of your hand if needed. Wrap with plastic wrap and form into a rough disc. Chill at least 30 minutes.
Make the filling
- Preheat oven to 425℉. Toss apple slices with flour, salt and spices, and honey and gently toss until evenly coated.
Make the streusel topping
- Make the streusel topping by putting all of the ingredients into the food processor and pulsing just until it looks like wet sand and clumps together.
To assemble
- Working on a large piece of floured parchment paper, roll out the larger portion of dough for the crust with a floured rolling pin, ensuring the dough is rolled out large enough to have at least a ½ inch overhang when fitted into the pie plate, flouring as needed to prevent sticking. Place into pie plate, using the parchment to help lift the crust.
- Evenly pour the apple mixture into the crust, and press down lightly. Trim the excess dough from the pan and crimp your edges. Top evenly with the streusel topping.
- Place pie on a baking sheet to catch any drips. For an extra shiny crust, use a pastry brush to brush egg wash around the crust edge, being careful to not get any on the pie plate.
- Bake for 25 minutes. Reduce heat to 350℉ and bake for another 40 – 50 minutes, until the crust is browned and juices bubble up through the steam vents. If the crust starts getting too brown after the first 25 minutes, cover the crust with a pie protector or foil. Let cool completely before cutting.
Notes
-
- Tips to ensure a flaky crust: Keep all ingredients as cold as possible. I will even float an ice cube in my water to keep it ice cold. Handle the dough as little as possible. Using the plastic wrap to bring the dough together helps to keep the dough cold and reduces the chances of over handling the dough. Patting it out into a thin disk before refrigerating the dough will make rolling it out later much easier than if you were to refrigerate the dough in a ball.
-
- If the dough becomes too soft while working with it, put it back in the fridge to chill.
-
- To make the crust without a food processor: In a medium mixing bowl, whisk together the flour and salt. Place the mixing bowl with the flour into the freezer while you get everything else together. Cut the butter into the flour using a pastry blender. Add the vanilla extract, honey and vinegar or vodka, and mix quickly. Add water slowly, a tablespoon at a time, mixing with hands until no powdery flour remains. Continue with next step.
-
- This crust recipe doubles well for a double crust pie.
-
- Pecans or walnuts (chopped) can be added to the streusel topping for extra crunch.
-
- If you don’t want to make your own crust, this filling recipe will also work perfectly with a store bought crust.
-
- For a deep dish pie: Use 3 pounds Honeycrisp, 1 Granny Smith, and 4 tablespoons flour.
Nutrition
This recipe was originally posted in September 2023 and was updated in September 2024.
Would this work with a gluten free graham cracker crust?
I haven’t personally tried it, but I think that would work! Keep me posted if you decide to try it out :)