Peel and core the apples, then cut them into small cubes measuring approximately 1/4 inch. Keeping the pieces relatively uniform encourages even cooking while preserving a pleasant texture in the finished jam.
Place the 4 cups of diced apples in a bowl and toss them thoroughly with the freshly squeezed lemon juice. Add the granulated sugar and stir until the apple pieces are evenly coated.
Cover the bowl and allow the apples to macerate for a minimum of 2 hours. Alternatively, refrigerate the mixture overnight. During this resting period, the sugar draws liquid from the apples and develops the fruit mixture before cooking.
Transfer the macerated apples and all of the accumulated juices to a jam pot. Add the 2 cups of whole fresh cranberries and place the pot over medium-high heat.
Cook the mixture for approximately 6–10 minutes, stirring frequently. Continue until the jam begins to thicken and the cranberries have burst and largely broken down. The diced apple pieces should remain mostly intact.
Remove the jam from the heat while its consistency is still slightly looser than desired, since it will continue to thicken as it cools.
Ladle the hot cranberry apple jam into prepared jars, leaving 1/4 inch of headspace at the top of each jar.
For long-term storage, process the filled jars in a water-bath canner for 10 minutes. At elevations above 6,000 feet, process the jars for 15 minutes.
Place the processed jars on a towel and allow them to cool completely. Once cooled, check each jar to confirm that it has sealed properly.
Store sealed jars in the pantry. Any jar that does not seal should be refrigerated. Refrigerate the jam after opening.