Simple Apple Butter Linzer Cookies

Here are my apple butter linzer cookies, with a homemade spiced apple butter filling tucked between tender almond cookies, and a light dusting of powdered sugar on top.

These cookies have become a favorite in my house during fall and winter. I love making a big batch because they keep well in an airtight container, and honestly, they taste even better the next day when the apple butter has had time to soften the cookies just a bit.

What Kind of Apples Should I Use?

For apple butter, you’ll want to use apples that break down easily and have a good balance of sweet and tart flavors. Classic choices like Fuji, Gala, or Honeycrisp work really well because they’re naturally sweet and cook down into a smooth, spreadable consistency. If you prefer a bit more tang in your apple butter, try mixing in a Granny Smith or two with your sweeter apples. The recipe calls for red apples, but honestly, any combination of your favorite apples will work – just avoid varieties that stay too firm when cooked, like Red Delicious, since they won’t break down as nicely into that smooth, buttery texture you’re going for.

Options for Substitutions

This recipe has some room for swaps if you need to work with what you’ve got:

• Red apples: Any apple variety works for the apple butter – try Granny Smith for a tarter flavor, Honeycrisp for extra sweetness, or whatever you have on hand. Just avoid super soft apples that might turn mushy.
• Flax eggs: If you’re not vegan, regular eggs work great (use 2 large eggs). For another vegan option, try chia eggs using the same ratio – 2 tablespoons chia seeds with 6 tablespoons water.
• Vegan butter: Regular butter is fine if you’re not keeping these vegan. You can also use coconut oil, though it may give a slight coconut flavor.
• Pastry flour: All-purpose flour works in a pinch, though your cookies might be slightly less tender. Use the same amount and don’t worry about it.
• Almond flour: You can substitute with more pastry flour if you have nut allergies, but the cookies will have a slightly different texture. Oat flour also works as a nut-free option.
• Vanilla bean paste: Regular vanilla extract is perfectly fine – use the same amount. The paste just adds those pretty vanilla specks.
• Apple cider vinegar: White vinegar or lemon juice can step in here. You just need something acidic to balance the sweetness.

Watch Out for These Mistakes While Baking

The biggest mistake when making linzer cookies is rolling the dough too thin, which causes them to break apart when you try to sandwich them together – aim for about 1/4 inch thickness so they’re sturdy enough to handle.

Since you’re making homemade apple butter, resist the urge to rush the cooking process by cranking up the heat, as this can cause it to burn and taste bitter instead of developing that deep, caramelized flavor you want.

When cutting out your cookies, dip your cookie cutter in flour between each cut to prevent sticking, and make sure your apple butter has cooled completely before spreading it on the cookies, otherwise it’ll make them soggy.

One more tip: dust the powdered sugar on top just before serving rather than storing them that way, since the moisture from the apple butter will dissolve the sugar and leave you with a sticky mess.

What to Serve With Apple Butter Linzer Cookies?

These cookies are perfect alongside a hot cup of coffee or tea for an afternoon snack, especially during the fall and winter months. I love setting them out on a platter with other holiday cookies like gingerbread or shortbread when I’m having friends over. They also pair really nicely with a scoop of vanilla ice cream or some whipped coconut cream if you want to turn them into a dessert. For a cozy breakfast or brunch spread, try serving them with hot apple cider or a chai latte.

Storage Instructions

Store: These cookies stay fresh in an airtight container at room temperature for about 5 days. Just make sure they’re completely cool before stacking them, and you can add a piece of parchment paper between layers to keep them from sticking together.

Freeze: Linzer cookies are great for freezing! You can freeze them assembled or keep the cookies and apple butter separate. Either way, use a freezer-safe container and they’ll last up to 3 months. If you freeze them assembled, thaw at room temperature for about 30 minutes before serving.

Make Ahead: The apple butter can be made up to 2 weeks ahead and stored in the fridge in a sealed jar. The cookie dough also freezes well for up to a month, so you can roll it out and bake fresh cookies whenever you want. Just let the dough thaw in the fridge overnight before rolling.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 2300-2500
• Protein: 20-24 g
• Fat: 65-75 g
• Carbohydrates: 420-450 g

Ingredients

For the apple butter:

• 3 large red apples (Honeycrisp or Gala work well)
• 1 tsp ground cinnamon (freshly ground preferred)
• 1.75 cups apple juice
• 2 tbsp apple cider vinegar
• 1/4 tsp nutmeg
• 1/8 tsp salt
• 1/2 cup brown sugar

For the cookie dough:

• 1 tsp ground cinnamon
• 2 tsp vanilla bean paste (or 1 tsp vanilla extract for deeper flavor)
• 1/2 cup ground almond flour
• 1/2 cup vegan butter (I use Earth Balance)
• 2 flax eggs (whisk 2 tbsp ground flaxseed with 6 tbsp water, let sit 5 minutes)
• 2.5 cups pastry flour (I prefer King Arthur)
• 1/4 tsp salt
• 1 cup powdered sugar

For finishing:

• 1/4 cup powdered sugar (for dusting)

Step 1: Make the Apple Butter Base

• 3 large red apples
• 1.75 cups apple juice
• 2 tbsp apple cider vinegar
• 1/2 cup brown sugar
• 1 tsp ground cinnamon
• 1/4 tsp nutmeg
• 1/8 tsp salt

Cut the apples into quarters (no need to peel), then combine them with apple juice and apple cider vinegar in a large pot.

Bring to a boil over medium-high heat, then reduce to a simmer and cook uncovered for 30 minutes, stirring occasionally, until the apples are completely softened and breaking apart.

Add the brown sugar, cinnamon, nutmeg, and salt, then use an immersion blender to puree the mixture until completely smooth.

This is where the magic happens—you’re building concentrated apple flavor that will be the heart of these cookies.

Step 2: Reduce Apple Butter to Thick Consistency

• apple butter mixture from Step 1

Pour the blended apple mixture back into the pot and cook uncovered over medium heat for 20-30 minutes, stirring every 5-10 minutes to prevent sticking on the bottom.

You’re looking for it to thicken significantly and darken in color—it should look glossy and jammy, and when you drag a spoon through it, the track should hold for a moment before filling back in.

Once it reaches this consistency, transfer it to a small bowl to cool completely while you prepare the dough.

I like to make the apple butter a day ahead so it’s completely cooled and thickened before assembly.

Step 3: Prepare the Flax Eggs and Cream Butter with Sugar

• 2 flax eggs
• 1/2 cup vegan butter
• 1 cup powdered sugar
• 2 tsp vanilla bean paste

While the apple butter cooks, prepare your flax eggs by whisking 2 tablespoons of ground flaxseed with 6 tablespoons of water and letting it sit for 5 minutes until thickened.

In a separate large bowl, cream together the vegan butter and 1 cup of powdered sugar, beating for about 2 minutes until light and fluffy—this aerates the dough and creates a tender cookie.

Add the prepared flax eggs and vanilla bean paste (or vanilla extract), mixing until fully incorporated.

This mixture will be the base for your dough.

Step 4: Mix Dry Ingredients and Combine with Wet Mixture

• butter-flax-vanilla mixture from Step 3
• 2.5 cups pastry flour
• 1/2 cup ground almond flour
• 1/4 tsp salt

In a separate bowl, whisk together the pastry flour, ground almond flour, and salt.

Add the dry ingredient mixture to the butter-egg mixture from Step 3, folding gently until just combined—don’t overmix, as this keeps the cookies tender.

The dough should come together but still feel slightly crumbly.

Transfer to plastic wrap, flatten into a disk, and refrigerate for 10-15 minutes until firm enough to roll without sticking.

This rest time allows the flour to fully hydrate and helps prevent shrinking during baking.

Step 5: Roll, Cut, and Bake the Cookies

• chilled dough from Step 4

Preheat your oven to 350°F while the dough chills.

Once chilled, roll the dough between two sheets of parchment paper to about 1/2 inch thick—this thickness is crucial for getting tender centers with slightly crispy edges.

Cut out cookies using your favorite shapes (Linzer cookies are traditionally heart-shaped, with half having a cutout window in the center).

Place on parchment-lined baking sheets and bake for 10-12 minutes until the edges are lightly golden but the centers still look slightly underdone—they’ll continue to set as they cool.

I find that slightly underbaking these creates the best tender texture.

Step 6: Cool Cookies and Prepare for Assembly

• baked cookies from Step 5
• 1/4 cup powdered sugar

Let the baked cookies cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.

Once cooled, dust the cookies with the window cutouts (the top cookies) generously with the 1/4 cup powdered sugar—this creates an elegant snowy effect that shows off the apple butter filling below.

Make sure the apple butter from Step 2 is completely cooled before moving to the final assembly.

Step 7: Assemble and Finish the Linzer Cookies

• cooled apple butter from Step 2
• cooled cookies from Step 6

Spread or pipe about 1-2 teaspoons of the cooled apple butter onto the flat side of each solid cookie (the bottom cookies).

Top with a dusted cookie, placing it flat-side-down so the window shows off the apple butter filling beneath.

The contrast between the tart apple butter, tender almond-flour cookie, and snowy powdered sugar makes these truly special.

Store in an airtight container at room temperature for up to 5 days.

Simple Apple Butter Linzer Cookies

Delicious Simple Apple Butter Linzer Cookies recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 33 minutes mins

Cook Time 1 hour hr 7 minutes mins

Total Time 1 hour hr 40 minutes mins

Servings: 4

Calories: 2400

Ingredients Method

Ingredients

  

For the apple butter:

• 3 large red apples (Honeycrisp or Gala work well)
• 1 tsp ground cinnamon (freshly ground preferred)
• 1.75 cups apple juice
• 2 tbsp apple cider vinegar
• 1/4 tsp nutmeg
• 1/8 tsp salt
• 1/2 cup brown sugar

For the cookie dough:

• 1 tsp ground cinnamon
• 2 tsp vanilla bean paste (or 1 tsp vanilla extract for deeper flavor)
• 1/2 cup ground almond flour
• 1/2 cup vegan butter (I use Earth Balance)
• 2 flax eggs (whisk 2 tbsp ground flaxseed with 6 tbsp water, let sit 5 minutes)
• 2.5 cups pastry flour (I prefer King Arthur)
• 1/4 tsp salt
• 1 cup powdered sugar

For finishing:

• 1/4 cup powdered sugar (for dusting)

Method

 

1. Cut the apples into quarters (no need to peel), then combine them with apple juice and apple cider vinegar in a large pot. Bring to a boil over medium-high heat, then reduce to a simmer and cook uncovered for 30 minutes, stirring occasionally, until the apples are completely softened and breaking apart. Add the brown sugar, cinnamon, nutmeg, and salt, then use an immersion blender to puree the mixture until completely smooth. This is where the magic happens—you're building concentrated apple flavor that will be the heart of these cookies.
2. Pour the blended apple mixture back into the pot and cook uncovered over medium heat for 20-30 minutes, stirring every 5-10 minutes to prevent sticking on the bottom. You're looking for it to thicken significantly and darken in color—it should look glossy and jammy, and when you drag a spoon through it, the track should hold for a moment before filling back in. Once it reaches this consistency, transfer it to a small bowl to cool completely while you prepare the dough. I like to make the apple butter a day ahead so it's completely cooled and thickened before assembly.
3. While the apple butter cooks, prepare your flax eggs by whisking 2 tablespoons of ground flaxseed with 6 tablespoons of water and letting it sit for 5 minutes until thickened. In a separate large bowl, cream together the vegan butter and 1 cup of powdered sugar, beating for about 2 minutes until light and fluffy—this aerates the dough and creates a tender cookie. Add the prepared flax eggs and vanilla bean paste (or vanilla extract), mixing until fully incorporated. This mixture will be the base for your dough.
4. In a separate bowl, whisk together the pastry flour, ground almond flour, and salt. Add the dry ingredient mixture to the butter-egg mixture from Step 3, folding gently until just combined—don't overmix, as this keeps the cookies tender. The dough should come together but still feel slightly crumbly. Transfer to plastic wrap, flatten into a disk, and refrigerate for 10-15 minutes until firm enough to roll without sticking. This rest time allows the flour to fully hydrate and helps prevent shrinking during baking.
5. Preheat your oven to 350°F while the dough chills. Once chilled, roll the dough between two sheets of parchment paper to about 1/2 inch thick—this thickness is crucial for getting tender centers with slightly crispy edges. Cut out cookies using your favorite shapes (Linzer cookies are traditionally heart-shaped, with half having a cutout window in the center). Place on parchment-lined baking sheets and bake for 10-12 minutes until the edges are lightly golden but the centers still look slightly underdone—they'll continue to set as they cool. I find that slightly underbaking these creates the best tender texture.
6. Let the baked cookies cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely. Once cooled, dust the cookies with the window cutouts (the top cookies) generously with the 1/4 cup powdered sugar—this creates an elegant snowy effect that shows off the apple butter filling below. Make sure the apple butter from Step 2 is completely cooled before moving to the final assembly.
7. Spread or pipe about 1-2 teaspoons of the cooled apple butter onto the flat side of each solid cookie (the bottom cookies). Top with a dusted cookie, placing it flat-side-down so the window shows off the apple butter filling beneath. The contrast between the tart apple butter, tender almond-flour cookie, and snowy powdered sugar makes these truly special. Store in an airtight container at room temperature for up to 5 days.