Don't forget that a trip through the desert or when he is sleeping/just waking will force him to be out of his armor. One will heat him up and dehydrate him while the other is because metal armor is really uncomfortable to sleep in.
I have a player who wears plate armour too. Problem is the campaign takes place mostly in a desert lol. I looked for rules on how to deal with heat damage with plate armour but couldn't find anything. What would you suggest?
That their basic concept is probably not all that logical in real world terms.
However, unless the option is not available, Endure Elements is a 0 level spell that lasts 24 hours, so any character in plate would probably contrive to gain access to it. Otherwise, the player is going to look for (and find) heat resistance.
If you do want to try to impose penalties, consider:
Discretionary: The GM can apply a –4 to +4 modifier to represent circumstances not covered by an existing rule. For example, he might apply +2 when a character makes an Impress check after a moving comment, or –4 when trying to direct a horse into a pitch black cave (–1) to escape trebuchet attacks falling nearby (–3). The GM is encouraged to use discretionary modifiers to make any skill attempt more interesting.
When heat damage is inflicted by an extreme environment (i.e. a heat wave), an exposed character makes a Survival check (DC 20). With success, he suffers 1d6 subdual damage every four hours; otherwise, he suffers 1d6 subdual damage every hour.
So, by the RAW, the most reasonable interpretation is that the character faces a Survival DC 20 check with a -4 penalty when he braves the heat.