How can I allow phoenixes to reproduce without overpopulation?

Since reproduction is a rare opportunity and very costly in energy to the mother bird, the females are exceedingly picky in choosing mates and courtships can last for decades before the deed is done.

The newly laid phoenix eggshell is, of course, blindingly valuable as a material for both jewellery and magic, so nest robbing and capturing mature birds for egg operations is a real threat.

Whenever a phoenix is reborn, the egg is indestructible until the bird is ready to hatch. Of course someone had the idea of capturing some phoenices, killing them at the same time, and putting their reborn eggs to support some massive piece of stone for a stunningly extravagant display for a never-ending cycle of flameburst, ashes, eggs, crack, splat, repeat.

Should a phoenix ever witness anything (great injustice, terrible cruelty, legendary stupidity) that offends it deeply enough, it will burst into flames on the spot and never rise from the ashes again.

So if the phoenixes ever discover 4chan they'll instantly go extinct? :P

The internet in general would be something of a Death World

Hmm, I don't know, what about all the bad stuff that was around before the Internet?

Wondermark says "a conservatory of Phoenices".

You could have them lose the ability to regenerate after they mate.

Maybe turn the phoenixes are fire idea up to eleven? When they get physical you get two birds merging into one larger hungrier bird, and they can "seed" baby phoenixes should they find the right conditions. Presumably they "feed" off some mystical energy source.

Another idea: the total biomass of pheonixes is fixed. Everytime a new one is laid all existing phoenixes shrink a little. In the present day they've bred themselves microscopic.

Are Phoenixes just magical animals or are they something more?

To me this seems like a kind of bizarre question. Sort of like saying, the gods are immortal and can breed, why don't they outnumber us?

It's not a question that usually comes to mind.

Phoenix are gods so far above organic life they don't even breathe the same kind of air. Their domain transcends time and space as we know them. Their reproduction represents the endless variety possibilities of the universe.

If they are sapient, they could decide to stop having offspring when their population gets too large. Maybe when their food begins to be depleted the ruling bird(s) outlaw breeding.

Another idea: Someone discovers a way to kill them in such a way they can't regenerate, so people begin hunting them for sport.

Because abstinence-based birth control works so well for the sapients we're familiar with...:P

These are mythical beings, they could probably do it.

Phoenixes that have reached a certain age start cooling over the centuries until they turn into a frost phoenix. A frost phoenix is on its last life, can't regenerate and it knows it. While this can happen naturally due to old age/ it being 'their time', it is far more common for a phoenix to consciously force the transformation because they have lost the will to live. This can be from imprisonment, ennui or losing a loved one, among others.

Once a phoenix turns it lives its remaining life as if each second was its last, whilst losing any and all instincts for self-preservation. This is very bad for your health if you are responsible for the phoenix's transformation, since not only are they just as powerful as they were before, they have no restraint whatsoever and explode in a concussive blast of ice upon death.

Phoenixes were created by the Fates to show the gods who really controls life and death. As soon as it was created, Zeus struck it with a lightning bolt only for it to reform, and the Fates just kind of smiled. Or so I read...somewhere. I can't remember where.

Phoenix was co-opting from Kemet's folklore if that's what you're taking about. If you're just trying to come up with answers, that's a pretty good one.