In this Perspective, the authors discuss the need for more sustainable and scalable ways of incentivising pharmaceutical industry innovation in response to infectious disease threats to public health. The authors consider incentives for innovation both in the current context of the COVID-19 crisis, and in the context of preventing other emerging or re-emerging infectious disease threats from becoming crises further down the line. The paper discusses the potential for innovative financial instruments, such as subscription-based models and bond-based approaches, to act as incentives. The authors also highlight the need to tackle a range of critical success factors beyond financial considerations. This includes tackling issues related to data access and the governance of data sharing, securing appropriate clinical trials infrastructure, ensuring suitable approval processes and procurement practices, and planning for manufacturing and supply chain capacity to mitigate against unintended consequences in affordability and access. Finally, the authors observe that the pharmaceutical industry will need to engage with society in ways that extend beyond producing a pill, diagnostic test or vaccine, in order to deliver on commitments made in response to any incentive systems that are put in place.