In a large skillet, heat the olive oil over medium heat. Add the sliced onions and a pinch of salt. Cook, stirring occasionally, for about 15-20 minutes until the onions are soft and golden brown.
Once the onions are caramelized, stir in the balsamic vinegar, honey, thyme, and season with salt and pepper. Cook for an additional 2-3 minutes until the liquid has evaporated. Remove from heat and set aside.
Preheat your oven to 400°F (200°C).
Place the whole wheat flatbread on a baking sheet lined with parchment paper. Spread the softened goat cheese evenly over the flatbread.
Top the goat cheese with the caramelized onion mixture, spreading it out evenly.
Place the flatbread in the preheated oven and bake for 10-12 minutes, or until the flatbread is warm and slightly crispy.
Remove the flatbread from the oven and top with fresh arugula for a pop of color and freshness.
Allow the flatbread to cool for a couple of minutes before slicing it into wedges. Serve warm.