Preheat oven to 400°F.
Place pastry rounds on a parchment-lined baking sheet and prick all over with a fork. Divide the cheese among pastry rounds. Top each pastry with slices of fennel and layer slices of beet on top (beets will shrink a little as they cook). Season with salt and pepper.
Bake until pastry is golden brown and slightly puffed, 13 to 15 minutes.
Garnish with fresh thyme and drizzle of honey. Serve warm.