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.
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.
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.
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.
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.
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.
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.