Jam crystallises over time because its sugar concentration sits very close to the limit of what the water in it can hold dissolved. In a mixture that close to saturation, even a small trigger can send sugar molecules back into crystal form.
What actually triggers the crystallisation?
Lemon juice is rarely added to jam recipes for no reason; the acid breaks part of the sucrose down into glucose and fructose, which makes it harder for those two sugars to crystallise again. If not enough lemon juice is added, the jam crystallises more easily over time.
Overcooking is another cause; if jam is boiled longer than needed and reduced too far, the sugar concentration rises higher than it should, creating ideal conditions for crystals to form. Sugar grains left stuck to the lid or a spoon can also act as a seed that triggers a chain reaction of crystallisation.
How is crystallisation prevented?
Sticking to the amount of lemon juice a recipe calls for is the most basic safeguard against crystallisation. Not cooking the jam longer than necessary, and checking its consistency early, also reduces the same risk.
Wiping the jar's rim and lid clean before sealing keeps stray sugar crystals from triggering new crystallisation. Sealing the jam once it has cooled completely rather than while still hot also stops evaporating moisture from condensing unevenly inside the lid.
Fluctuations in storage temperature can speed up crystallisation too; a jar kept at a steady, cool temperature stays smooth for much longer than one left somewhere that keeps warming up and cooling down.
Crystallised jam is generally still fine to eat and is not dangerous; warming the jar gently and stirring usually dissolves most of the crystals and brings the jam back close to its original consistency.
The fruit's own pectin content used in the jam plays an indirect role too; recipes made with low-pectin fruit may need extra sugar, which raises the overall sugar concentration and slightly increases the risk of crystallisation. Recipes using commercial pectin powder can reach the same set with less sugar, so the crystallisation risk stays comparatively lower.
How often the jar is exposed to air after opening matters too; every time it is opened, a little surface moisture evaporates and the remaining sugar concentration slowly climbs. That is why a jar in frequent use can start crystallising earlier than one that has never been opened; sealing the lid tightly and returning it to the fridge quickly reduces this effect.
Freezer jam, which is usually not boiled at all, tends to have a lower sugar concentration than classic cooked jam, which greatly reduces the risk of crystallisation. However, because it has never been boiled, this type of jam has a much shorter shelf life and cannot be kept for long outside the freezer.