Chop the apples and cranberries together on a clean cutting board until they reach the desired consistency. Pour into a clean glass bowl and add the sucanat, salt, and whey. Mix together with a wooden spoon, smashing the mixture to get the juices flowing.
Pack the mixture of apples and cranberries into a sanitized quart jar. Using your hand or a spoon, press the contents down to submerge the mixture, leaving about 1 inch of space at the top of the jar. Cover tightly with an airlock fermenting lid.
Leave on the counter, away from direct sunlight and drafts, for 2 to 3 days. Once the relish is ready, cover with a regular lid and place in refrigerator until needed.