Toss the peaches and nectarines together in a large kettle or stockpot. If you’re using frozen fruit, add any of the juice accumulated when the fruit thaws.
Add the brown sugar, raisins, mustard seed, cinnamon, nutmeg, cloves, and vinegar. Stir to blend together.
Cook over medium-low heat until the sugar is completely dissolved, about 15 minutes, stirring occasionally.
Raise the heat to medium and cook until the chutney has thickened, about 45 minutes to an hour. As the chutney thickens, stir it frequently to prevent the fruit from sticking to the bottom of the pan.
Remove the pan from the heat and stir in the toasted pecans, mixing evenly into the chutney.
Ladle the chutney into sterilized jars, leaving ¼” of room from the top, known as headspace. Secure the lids and process in a water bath or refrigerate.
Serve the chutney warm or chilled