City planning, improvements in personal hygiene and medical innovations over the past two centuries led to the decline in infectious disease mortality in most parts of the world. As a consequence of this so-called epidemiological transition, modern public health concerns and policies have become increasingly structured around non-communicable diseases (NCDs), such as diabetes, obesity or hypertension. It is in this context that the new type of coronavirus (COVID-19) emerged from Wuhan, China, in late 2019. More than 3 million deaths worldwide as of May, 2021 combined with often low levels of transparency regarding the availability of PCR tests or the development and distribution of vaccines have considerably damaged the trust in modern healthcare systems around the world. COVID-19, a zoonotic disease, illustrates the systemic vulnerability and inflexibility of modern, anthropocentric infrastructures such as public healthcare systems. The causal relation between primary (viral) and multiple secondary (bacterial) infections in overloaded hospital settings is an obvious example. In this essay, we start from the medical notion of resilience to discuss the importance of coexistence with microorganisms for a more resilient healthcare system, by which we mean a social-ecological system. The two different cases, 2009H1N1 influenza and antimicrobial resistance, introduced and discussed here are related to the COVID-19 pandemic in important systemic ways and will allow us to highlight three aspects of resilience in healthcare: (1) plasticity, (2) diversity and (3) sustainability. In the last section, we discuss the concept of planetary health that we hope can help us imagine better ways of protecting the health of both humans and the planet in pandemic and post-pandemic times.