Holothuria atra is an omnivore, sifting through the sediment with its tentacles and feeding on detritus and other organic matter. It ingests sand at the same time and digests the biofilm on the sand grains before ejecting them through its anus.[5]
As a defence against predators, Holothuria atra emits a toxic red fluid when its skin is rubbed or damaged.[2] When attacked, it does not eject Cuvierian tubules in the way that some sea cucumbers do, but instead extrudes its internal organs through its anus. These are also toxic and this sea cucumber is not recommended to be kept in a reef aquarium because the water may become toxic to its other animal occupants.[5]
It is not possible to distinguish between male and female Holothuria atra externally. Maturity is reached at a body length of about 16 centimetres (6.3 in) and spawning mostly takes place during the summer and autumn although in equatorial waters it may take place all year round.[6] Holothuria atra is also fissiparous, meaning that it can reproduce by transverse fission.[3][7] It is mostly smaller individuals that divide in this way. A constriction appears, becomes deeper and deeper and after some time the integument separates leaving two relatively wide but short individuals.[4] No sand adheres to the newly separated surfaces as there are no tube feet present to retain the grains.[4]