The stomach content of 60 krill specimens from the Southern Ocean were analyzed for the presence of micro-plastic (MP), by testing different sample volumes, extraction approaches, and applying hyperspectral imaging Fourier-transform infrared spectroscopy (μFTIR). Strict quality control was applied on the generated results. A high load of residual materials in pooled samples hampered the analysis and avoided a reliable determination of putative MP particles. Individual krill stomachs displayed reliable results, however, only after re-treating the samples with hydrogen peroxide. Before this treatment, lipid rich residues of krill resulted in false assignments of polymer categories and hence, false high MP particle numbers. Finally, MP was identified in 4 stomachs out of 60, with only one MP particle per stomach. Our study highlights the importance of strict quality control to verify results before coming to a final decision on MP contamination in the environment to aid the establishment of suitable internationally standardized protocols for sampling and analysis of MP in organisms including their habitats in Southern Ocean and worldwide.