A. percula is associated specifically with Heteractis magnifica and Stichodactyla gigantea, and as larvae use chemical cues released from the anemones to identify and locate the appropriate host species to use them for shelter and protection.

The Great Barrier Reef Marine Park Authority regulates the number of collection permits issued to aquarium fish dealers who seek this, and other tropical fish within the Great Barrier Reef Marine Park.

A second hypothesis is that A. percula has acquired immunity towards the sea anemone's toxins, and a combination of the two has been shown to be the case.

At night time the moon maintains a higher level of alertness in A. percula and this increases the interaction with the males and females.

Unlike nonreproductives in some animal groups, they cannot obtain occasional breeding opportunities, because their gonads are not functional.

The fish lay their eggs in a safe spot close to the anemone from where they are easily protected, and the parents can retreat to safety if danger threatens.

Anemonefish usually lay their nests in the evening after a few days of carefully cleaning and examining the chosen site.

Preferred egg sites are flat or slightly curved rocks or some other item the fish have dragged near their nest for the purpose.

At hatching, the larvae burst free and swim up toward the moonlight and the open ocean to ride the currents and eat plankton for about a week, before the still tiny metamorphosed clowns return to the reef and look for an anemone in which to settle.

Recruitment is the number of individuals in a given species that can survive within a certain amount of time following larval habitation.

[10] The higher the level of recruitment, the better chance a larva has of surviving long enough to become an adult fish.

Large food supplies, low predator threats, and the availability of nearby anemones are all factors that affect their recruitment levels.

A. percula, like most coral reef fish, has a bipartite lifecycle, which has a scattering pelagic larval stage, whereas its resident phase is motionless.

Anemonefish are known for reproducing all year round when they are in lower latitudes and recruitment with these fish is anticipated to follow the same pattern.

[10] Anemonefish are specialized coral reef fish that live within host anemones and are found in warmer waters in the Pacific and Indian Oceans, off northwest Australia, southeast Asia, and Japan.

Unless a significant size difference exists, two anemonefish species show aggression towards each other when trying to occupy the same host anemone.

[10] This is why the supply of nearby anemone hosts so strongly influences A. percula’s ability to achieve recruitment and survival in general.

[10] A study done by Elliot & Mariscal in the region of Madang, Papua New Guinea found that all of the H. magnifica anemones that were censused were occupied by A. percula and A. perideraion.

Shallow waters are not an inhabitable environment for A. percula because of the lower salinity levels, increased temperatures, and exposure during low tides.

A. percula cleans the host anemone by consuming algae residue and zooplankton such as copepods and larval tunicates.

Impairment of larval olfaction may also make them less able to locate appropriate reef habitats at the higher levels of ocean acidification that are projected to occur with increased carbon dioxide emissions.

[12] A paper published in Nature in 2020 cast doubt on the effect of acidification, stating "our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO2 oceans".

After hatching, the larvae are very small and are transparent except for the eyes, yolk sac, and a few colors across the body.