Pyrolysis-GC/MS is increasingly used to quantify microplastics (MP) in environmental samples. In general, prior to analysis, purification steps are carried out to reduce the environmental matrix in sediment samples. The conventionally used protocol of density separation followed by digestion of organic matter does not allow for complete isolation of MP from the associated organic and mineral matter. Among the pyrolysis products used as indicator compounds for plastic polymers, some may originate from other substances present in the environmental samples. In this paper, the indicator compounds are reviewed for the most common polymers: PE, PP, PS, PET and PVC and selected taking into account potential interactions with substances present in environmental matrices. Even after a purification step, a residual mineral fraction remains in a sediment sample, including matrix effects. This effect may be positive or negative, depending on the investigated polymer and is thus important to consider when using Pyr-GC/MS for the quantification of MP in sediment samples. It also shows that no external calibration can be used to reliably quantify MP in such samples and that the use of internal standards is compulsory.