Polycarbonate is a widely used polymer in food contact applications all around the world. However, due to the potential release of Bisphenol A (BPA) during repeated washing cycles, its use becomes compromised as BPA is known for being an endocrine disruptor for rodents. In order to tackle this issue, sol-gel coatings based on organoalkoxysiloxane were developed on PC, to act as a physical barrier. To this end, two sol-gel systems based on tetraethylorthosilicate (TEOS), methyltriethoxysilane (MTES) and 3-glycidyloxypropyltriethoxysilane (GPTES), three common sol-gel precursors, were prepared. The coatings derived from the latter two systems were then studied with regards to their potential toxicity in vitro. Migration tests were performed in food simulants, and the maximal migration was obtained in ethanol 10% (v/v) for one system and in isooctane for the other one. In vitro genotoxicity was assessed with the Ames test (OECD 471) and the micronucleus assay (OECD 487), and no genotoxic effect was observed. Moreover, the estrogenic activity of the extracts was studied with a transcriptional activation assay using transient transfection in human cells; none of the extracts was found estrogenic. These negative in vitro results are highly promising for the future use of these new barrier coating formulations onto food contact materials.