Pulse the tomatoes in a food processor, or dice into chunks.
Dice or food process the apples and onions.
Add the tomatoes, apples, and onions to a large pot on the stove, and simmer until most juices evaporate (this could take up to an hour, it depends on the water content in your tomatoes).
Once liquids are reduced, add the apple cider vinegar and chia seeds and stir well.
Let cool in a glass bowl or jar, and then refrigerate or freeze once cool.