In a medium, heavy-bottomed saucepan, combine the diced nectarines, chopped red onion, apple cider vinegar, brown sugar, grated ginger, mustard seeds, red pepper flakes, and salt.

Bring the mixture to a boil over medium-high heat, stirring occasionally to ensure the sugar dissolves completely.

Once boiling, reduce the heat to low, cover the saucepan partially (leaving a small gap for steam to escape), and simmer for 20 minutes, stirring every 5 minutes.

After 20 minutes, remove the lid completely and continue to simmer for another 10 minutes, or until the chutney has thickened significantly and the nectarines are soft but still hold some shape. It should coat the back of a spoon.

Remove the chutney from the heat and let it cool to room temperature. The chutney will thicken further as it cools.

Transfer the cooled chutney to an airtight container. Store in the refrigerator for at least 4 hours (or overnight) before serving to allow the flavors to meld properly. Best served chilled or at room temperature.