Set a large skillet (I like cast iron) over medium heat. Add the butter and 2 tbsp of olive oil. Once the butter is melted and beginning to foam, add the onions along with a generous pinch of salt. Stir to combine, cover the pot and cook, covered, for about 20 minutes - or until the onions have released a significant amount of moisture and have reduced in size.
Preheat oven ot 180°C/350°F. Remove the lid and cook, stirring every so often. until the onions are deeply browned and caramelised. If you notice the onions are sticking or browning too quickly, you can deglaze with a splash of water here and there. This should take another 20-30 minutes.
Stir in the thyme and nutmeg anf cook just until fragrant - only another minute or two. Scrape the onions into the bottom of the pie crust.
Meanwhile, add the eggs, milk, creme fraiche, a ¼ tsp of salt and a generous grind of black pepper to a large bowl. Whisk until thoroughly combined, or use a handheld blender to ensure everything is emulsified. Stir in the goat cheese and gruyere.
Pour the egg mixture over the onions into the prepared pie crust. Set the quiche on a rimmed baking tray and move to the oven. Bake for 30-40 minutes or until the centre wobbles only slightly when shaken. Remove and allow to cool for at least 15 minutes before serving.
Notes
I highly recommend making your own pie crust. Use my recipe - it includes blind baking instructions. You can use any leftover egg from the egg wash in the quiche.