The production and use of engineered nanomaterials and nano-enabled products is increasing, enabling innovations in many application areas, e.g., in the sector of food contact materials. However, nanosafety-relevant information for chemical risk assessment is still scarce, leading to a high level of uncertainty and making the early integration of safety to the innovation process indispensable. This study analyzed the strengths, weaknesses, and applicability of the nano-specific Safe-by-Design (SbD) concept using nanoclay-containing polymer coffee capsules as a theoretical case study. In addition, a material flow analysis was conducted to identify exposure pathways and potential risks, and a multi-stakeholder approach was applied to discursively discuss challenges when attempting to combine safety and innovation at an early stage. The results indicate that the SbD concept is generally welcomed by all stakeholders, but there is a lack of clear rules on the transfer of information between the actors involved. Furthermore, a voluntary, practical application usually requires in-depth knowledge of nanotechnology and often additional financial efforts. Therefore, incentives need to be created, as there is currently no obvious added value from a company’s point of view. The SbD concept should be further developed, standardized, and integrated into existing legal frameworks to be implemented effectively.