Over the last decade Japanese researchers have taken the lead in the emerging discipline of molecular robotics. This new technology aims to produce artificial molecular systems that can adapt to changes in the environment, self-organize and evolve. This paper explores the question of how to stimulate responsible research and innovation in the field of molecular robotics technologies. For this, we first draw lessons from earlier societal responses in Japan to emerging technologies, such as genetic engineering, nanotechnology, synthetic biology and genomic research. Next we describe various real-time technology assessment (TA) activities on molecular robotics in Japan to depict the state-of-the-art of the academic and public debate on the social aspects of molecular robotics. Lessons from earlier societal responses to emerging technologies demonstrated three potential challenges: finding and involving the ‘right’ experts and stakeholders, keeping regulations up to date, and getting scientists and citizens involved in science communication. A literature review, ‘future workshop’ and scenario workshop raised a number of ethical, social, political and cultural issues, and addressed desirable and undesirable scenarios for the next few decades. Twitter text mining analysis indicates that the level of attention, knowledge and awareness about molecular robots among a broader audience is still very limited. In conclusion, we identify four activities crucial to enable responsible innovation in molecular robotics—getting to grips with the speed of the development of molecular robotics, monitoring related technical trends, the establishment of a more stable TA knowledge base, and a sustained interaction between molecular roboticists and social scientists.