In a large saucepan, heat the olive oil over medium heat and add the onions, mustard seeds, and cinnamon. Stir to combine.
Saute the mixture until the onions are translucent, about 3 minutes.
Stir in the apples, pears, vinegar, apple juice, brown sugar, and fresh ginger, cook for 1 minute, then lower the heat and simmer until the apples and pears are just soft, about 20 to 30 minutes.