Microplastic (MP) pollution has been an emerging threat for marine ecosystems all around the globe with increasing evidence that even the world’s most remote areas such as the Arctic and Antarctica are no longer unaffected. However, only few of the studies that focused on Antarctic environments have been limited to living organisms and the entry mechanisms of MP into the Antarctic marine food webs and its impacts on it remain a widely unknown field of research. The goal of this study was to investigate the occurrence of MP in Emperor penguins (Aptenodytes forsteri), which represent the most southerly-situated penguin species on earth and are a top endemic predator in the marine environment of the Antarctic. To assess MP ingestion, the stomachs of sixteen Emperor penguin chicks from the Atka Bay colony (Weddell Sea) were dissected and stomach contents were screened visually for potential MP, which is a novel approach. Putative MP particles were chemically analyzed by applying Fourier Transform Infrared (FT-IR) based Attenuated Total Reflection (ATR) spectroscopy to determine their polymer type. A total of 51 microfibres and 11 particles of different colours and size classes were sorted out from the stomachs. However, none of them could be successfully assigned to a synthetic polymer. This suggests that MP have either not yet reached the local food web of the Weddell Sea, or that if they have, at least there is no biomagnification and trophic transfer occurring. Besides revealing information about MP ingestion, this study provided sample materials that serve as a basis for further studies on foraging behavior of the Emperor penguin.