Slice the yellow onion into thin half-moons. Heat 0.5 tablespoon of olive oil in a large skillet over low heat; add onions and a pinch of salt, cooking for 45 minutes while stirring occasionally until deeply browned and jammy.
While onions caramelize, dice the yellow potatoes into half-inch cubes. In a separate skillet, heat 0.5 tablespoon olive oil over medium heat and add potatoes. Cover and cook for 20 minutes, tossing occasionally until the exteriors are crispy and golden.
Dice the chicken breast into one-inch pieces and toss in a bowl with smoked paprika, dried thyme, half the sea salt, and half the black pepper.
Remove potatoes from the skillet; increase heat to medium-high and add the remaining 0.5 tablespoon of olive oil. Add the chicken, searing for 7 minutes until golden and cooked through, then remove and set aside.
Add sliced mushrooms, diced zucchini, and sliced red bell pepper to the skillet. Sauté for 8 minutes until tender-crisp, then stir in minced garlic for 1 minute.
In a small bowl, whisk the balsamic vinegar and dijon mustard together to create a low-calorie glaze.
Return the chicken, potatoes, and caramelized onions to the skillet. Pour the balsamic-mustard mixture over the top and stir for 2 minutes until the liquid reduces into a glossy glaze. Season with the remaining salt and pepper.