Preheat the oven to 350 degrees Fahrenheit. Line a baking sheet with parchment paper.
In a large bowl, combine coconut oil, maple syrup, molasses, and vanilla. Whisk to combine. Add almond flour, salt, and spices. Stir until dough forms. Allow dough to rest for about 3 minutes, then stir to combine again.
If dough seems too wet to roll into a ball, add 2-3 tablespoons more almond flour.
Using a tablespoon, scoop dough and roll into a ball (You don't want them to be bigger than this).
Roll into balls and place in even rows on baking sheet. Using your index finger, make an indention in the center no more than halfway down.
Bake for 12-14 minutes. With a spatula, transfer thumbprint cookies to wire rack and allow to cool completely.
While cookies are cooling, add dairy-free cream cheese, maple syrup, and vanilla to a small bowl. Using an electric mixer, beat until smooth. Place in refrigerator until cookies have baked and cooled.
Once cookies have cooled, fill each indention in the center of the cookie with the cream cheese frosting.
These gingerbread thumbprints are best the day they are made. Store in an airtight container in the refrigerator for 2-3 days.