Add flour, almond meal, flax seed, thyme, and cheese to a food processor. Pulse food processor to blend. Add one tablespoon of cold butter at a time, pulsing in between until dough is crumbly. Slowly drizzle about 4 tablespoons of ice water into dough mixture while the food processor is on. Stop adding water as soon as the dough is moist enough to start pulling off edges of the work bowl.
Place ball of dough onto parchment paper. Flatten into a thick disk, wrap the dough in the paper and chill in the refrigerator for at least one hour or overnight. After chilling, preheat oven to 350 degrees F.
Roll dough between two pieces of parchment paper until it is evenly 1/8 inch thick. Use pizza cutter to cut dough into squares or use small cookie cutters to punch out shapes. Place uncooked crackers on a parchment- lined baking sheet into the top one-third of the oven. Cook for 8-10 minutes until lightly golden brown. Let cool for 5 minutes. Store in air-tight container.