Combine beetroot, apples, onions, red wine vinegar, sugar, and all spices in a large saucepan.
Bring the mixture to a gentle simmer over medium heat, stirring occasionally to dissolve the sugar.
Continue cooking for approximately 1 hour, stirring regularly, until the beetroot is tender and the mixture has thickened.
Meanwhile, sterilize glass jars and lids in boiling water.
Spoon the hot chutney into sterilized jars, leaving ¼ inch headspace.
Seal jars immediately and allow to cool completely before storing.