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Step 1
Preheat oven to 400°. Heat butter in a large skillet over medium, swirling until foaming subsides. Arrange shallots in a single layer in skillet, flat or cut side down where possible. Season well with salt and cook, undisturbed, until deep golden brown underneath, about 5 minutes. Turn and cook until deep golden brown on the other side, about 5 minutes.
Step 2
Add vinegar and 1 cup water, then add thyme sprigs, chiles, and sugar and swirl skillet to combine. Bring liquid to a boil; reduce heat so liquid is at a simmer.
Step 3
Transfer skillet to oven and roast shallots, turning halfway through, until sauce is reduced to a glaze and a paring knife easily slides through centers, 35–40 minutes. Taste and season with more salt if needed.
Step 4
Spoon shallots and glaze into a serving dish and top with thyme leaves.
Step 5
Do Ahead: Shallots can be cooked 2 days ahead. Gently reheat in a large saucepan (or in the microwave in 30-second intervals) with a little water to loosen up glaze.