Prepare the jars. Begin by sterilizing your jars and lids. Boil them in water for at least 10 minutes, then keep them hot until ready to use.
Combine ingredients. In a large, non-reactive pot, combine diced apples, onion, raisins, brown sugar, apple cider vinegar, ginger, allspice, cloves, salt, and red pepper flakes. Bring the mixture to a boil over medium heat, stirring frequently.
Simmer. Reduce the heat and let the chutney simmer for about 45 minutes to 1 hour, or until it thickens. Stir occasionally to prevent sticking. You can briefly pulse in a food processor or with a stick blender if you’d prefer a smoother chutney
Fill jars. Once the chutney has thickened, remove it from the heat. Ladle the hot chutney into the prepared jars, leaving about ½-inch of headspace. Remove any air bubbles with a non-metallic spatula. Wipe the rims clean, then place the sterilized lids on the jars and screw on the bands until fingertip tight.
Process. Place the jars in a waterbath canner, making sure they are completely submerged in water. Bring the water to a boil and process the jars for 10 minutes. Adjust the processing time if you live at a high altitude.
Cool and store. After processing, remove the jars from the canner and let them cool on a towel for 12-24 hours. Check the seals before storing in a cool, dark place. The chutney will keep for up to a year.