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In recent years, due to modern techniques for the distribution, transport, and retail sale of food, the production of large amounts of non-biodegradable and bioaccumulative packaging waste has become a major environmental issue. To address this issue, new food packaging materials based on renewable biomass have been studied as eco-friendly, biodegradable, and biocompatible alternatives to synthetic materials. However, although these materials are not petrochemical derivatives, the presence of contaminants cannot be excluded. This work aims to extend the knowledge on bio-based packaging materials, researching the presence of contaminants potentially able to migrate to food at concentrations of concern. In this study, we focus on two classes of contaminants, organophosphate esters (OPEs) and perfluoroalkyl substances (PFASs), carrying out migration tests toward different simulants, according to the current European regulation. PFAS analysis was performed using high-resolution liquid chromatography coupled to ion trap-tandem mass spectrometry (QTrap). OPE analyses were performed both by gas chromatography-mass spectrometry (GC-MS) and high-resolution liquid chromatography coupled to triple quadrupole mass spectrometry (TQMS). Preliminary findings demonstrate the release of toxic OPEs and PFASs from bio-based food packaging, highlighting the need to investigate the presence of potentially harmful chemicals in these materials.