Sauté onion in olive oil for 5 minutes. Add garlic and bell pepper, cook 3 minutes.
Add mushrooms and cook until browned and moisture has evaporated, 4–5 minutes.
Add spinach and stir until wilted. Season with salt and pepper. Cool slightly.
Grease a 9x13 inch baking dish.
Layer half the bread cubes, half the vegetables, and half the cheese.
Repeat with remaining bread, vegetables, and cheese.
Whisk eggs, milk, cream, mustard, salt, pepper, and nutmeg until smooth.
Pour custard evenly over the dish. Press bread down to absorb liquid.
Cover tightly and refrigerate overnight or at least 8 hours.
Remove from fridge 30 minutes before baking.
Preheat oven to 175°C (350°F).
Bake uncovered 50–55 minutes until top is deep golden and center is set.
Rest 10 minutes before slicing.
Top with fresh chives and flaky sea salt. Serve warm.