Printing inks are commonly used in multilayer plastics materials used for food packaging, and compounds present in inks can migrate to the food either by diffusion through the multilayers or because of set-off phenomena. To avoid this problem, the right design of the packaging is crucial. This paper studies the safety by design of multilayer materials. First, the migration from four different multilayers manufactured using polyethylene terephthalate (PET), aluminium (Al) and polyethylene (PE) was determined. The structural differences among materials such as the presence of inks or lacquer coatings as well as the differences in layers position allowed the study of a safety-by-design approach. Sixty-nine different compounds were detected and identified; 49 of them were not included in the positive list of Regulation EU/10/2011 or in Swiss legislation and 15 belong to Cramer class III, which means that they have a theoretical high toxicity. Some of the compounds related to ink composition were pyrene, a compound commercially used to make dyes and dye precursors and the antioxidant Irganox 1300. The application of external lacquers decreased the concentration of some migrants but also brought the potential for new migrants coming from its composition. A final risk assessment of the material allowed evaluating food safety for different food simulants and confirm it.