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In a large skillet on medium heat add the butter and sliced onions.
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Add the thyme, salt and pepper to taste.
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Lower the heat to simmer and continue cooking until onions are golden for approximately 20-30 minutes.
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While cooking onions, place pine nuts in a small skillet and cook for 4-5 minutes until toasted.
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Stir toasted pine nuts into onion mixture.
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Preheat oven to 425 degrees.
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Rinse and dry the mushrooms.
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Remove stems.
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Place mushrooms caps, stem-side up on a baking sheet.
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Bake for 5 minutes.
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Turn mushrooms stem side up.
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Divide filling among cups.
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Bake 8-10 minutes.