Despite typically not being taken into account (usually in favour of the ‘global distillation’ process), the input of persistent organic pollutants (POPs) through biological activities can be indeed relevant at the local scale in terrestrial polar environments when seabird colonies are considered. Seabirds can bioaccumulate and biomagnify POPs, gather in large numbers and excrete on land during their reproductive season, thus making them locally as relevant secondary sources of POPs. The first part of this study indicated that these colonies act as so for several essential and non-essential trace elements, and this second part tests the same hypothesis concerning POPs using the very same samples. Lichens (n = 55), mosses (n = 58) and soil (n = 37) were collected from 13 locations in the South Shetlands Archipelago during the austral summers of 2013–14 and 2014–15. They were divided in colony (within the colony itself for soil and within and surrounding the colony for vegetation) and control (at least 150 m away from any colony interference) and analysed for POPs such as organochlorine pesticides, polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers and stable isotopes (C and N). Results showed that colonies act clearly as a secondary source for PCBs and likely for hexachlorobenzene. As in the first part, probable local sources other than the colonies themselves are hypothesised because of high concentrations found in control sites. Again, soil seemed the most adequate matrix for the intended purposes especially because of some particularities in the absorption of animal-derived organic matter by vegetation, pointed out by stable isotope analyses.