Preheat the oven to 175°C (350°F). Position a rack in the center. Heating the oven now ensures even baking later and gives you time to finish the savory components.

Heat a wide sauté pan over medium heat and add the olive oil and butter. When the butter foams, add the thinly sliced onions and a generous pinch of salt. Cook uncovered, stirring occasionally, for 20–30 minutes until deep golden-brown and jammy. Reduce the heat if the onions begin to brown too quickly. Why: Low-and-slow caramelization converts onion starches to sugars and develops complex, sweet-savory flavors; quick, high heat will burn the edges before the centers soften.

If the onions are taking too long or you want to coax sweetness, sprinkle 1 teaspoon granulated sugar over them at the 10-minute mark and continue cooking. Toward the end, add a splash (1–2 tablespoons) of water to deglaze the pan and scrape up any browned bits. Why: Sugar accelerates the Maillard reactions; deglazing captures the concentrated fond (browned bits) and reincorporates that flavor into the onions.

While the onions finish, grate the cheese and warm the milk in a small saucepan until it’s just steaming (do not boil). Warming the milk prevents a temperature shock when you combine it with the eggs and helps produce a silkier custard.

In a large bowl, whisk the eggs with the salt, pepper, thyme, and a pinch of nutmeg (if using). Whisk until smooth and slightly frothy—this incorporates air that lightens the texture slightly.

Temper the eggs: slowly pour about 60–90 ml (1/4–1/3 cup) of the warm milk into the eggs while whisking constantly, then gradually whisk in the remaining milk. Why: Tempering raises the eggs’ temperature gently so they don’t scramble when mixed with warm liquid; this keeps the custard uniform and silky.

Fold about two-thirds (100 g) of the grated cheese into the egg-and-milk mixture. This distributes cheese evenly through the custard so each bite is cheesy and cohesive.

Stir the caramelized onions to make sure they’re not overly wet. Spread them in an even layer in the buttered pie dish. Why: An even layer prevents pooling and ensures consistent texture and caramelized flavor in every slice.

Pour the egg-cheese custard over the onions, then scatter the remaining cheese on top. Lightly shake the dish to settle the custard. Why: Topping with cheese forms a golden, flavorful crust while the interior sets into a creamy custard.

Place the pie dish into a larger roasting pan. Pour hot (not boiling) water into the roasting pan to come halfway up the sides of the pie dish (a bain-marie). Carefully transfer to the oven and bake for 25–30 minutes, until the edges are set and the center jiggles slightly when shaken. Why: The water bath provides gentle, even heat around the custard, preventing overcooking and curdling so the interior stays silky rather than rubbery.

If you prefer a browner top, remove the water bath for the last 3–4 minutes and switch to broil with the oven door slightly ajar—watch carefully so the cheese doesn’t burn. Why: Direct radiant heat rapidly browns the cheese to develop nutty crust flavors, but it can go from perfect to charred within seconds.

Remove the dish from the oven and let it rest 10–12 minutes before slicing. Resting finishes the set and makes slicing cleaner. Garnish with a few fresh thyme leaves and a grinding of pepper, then serve warm.