Peel and thinly slice the yellow onion. Heat a medium skillet over medium-low heat and add 1 tablespoon olive oil and 1 teaspoon butter. Add the sliced onion and sprinkle 1 teaspoon salt and 1 teaspoon brown sugar over the top. Cook slowly, stirring every 3–5 minutes so they soften and release their sugars without burning. After about 10 minutes, add 2 tablespoons of water to deglaze the pan and continue cooking another 10–15 minutes until the onions turn deep golden-brown and jammy. Remove from heat and let cool slightly. Use 2 tablespoons for the sandwich; reserve any extra for another use (store refrigerated up to 4 days).

Sandwich and Assembly

Butter and mustard the bread

Spread 1 tablespoon of softened butter evenly over the outer side of each slice of sourdough. On the inside (non-buttered) side of one slice, spread 1 teaspoon Dijon mustard and, if using, 1 teaspoon whole-grain mustard on the other slice's inside.

Layer the cheeses and fillings

On the mustard-spread side of one slice, place the aged cheddar slices first (2 oz total), followed by the shredded Gruyère (1 oz) and the sliced fontina (1 oz). Distribute 2 tablespoons of the caramelized onion evenly over the cheese layers. Sprinkle fresh thyme leaves (1 teaspoon) and a little cracked black pepper to taste. If using, add pickled jalapeño slices or tomato slices and microgreens/arugula on top of the onions.

Close and press

Place the second slice of bread, buttered side out, on top to close the sandwich. Gently press to compact the layers so the cheeses contact each other and the bread.

Cook the sandwich

Heat a clean nonstick or cast-iron skillet over medium-low heat. Place the sandwich in the skillet, buttered side down. Cook for 3–5 minutes until the bottom is golden-brown and the cheese inside starts to melt. Carefully flip the sandwich using a spatula, press gently with the spatula or a heavy pan for 30–60 seconds, then cook another 3–4 minutes until the second side is golden and cheese is fully melted. If the bread browns too quickly before the cheese melts, lower the heat and cover the pan for 1–2 minutes to trap heat and hasten melting.

Rest and slice

Transfer the sandwich to a cutting board and let rest 1 minute to allow the cheese to set slightly. Slice diagonally or down the middle. Serve immediately with any remaining caramelized onions or optional sides.