Health policy and systems research (HPSR) is a multi-disciplinary, largely applied field of research aimed at understanding and strengthening the performance of health systems, often with an emphasis on power, policy and equity. The value of embedded and participatory HPSR specifically in facilitating the collection of rich data that is relevant to addressing real-world challenges is increasingly recognised. However, the potential contributions and challenges of HPSR in the context of shocks and crises are not well documented, with a particular gap in the literature being the experiences and coping strategies of the HPSR researchers who are embedded in health systems in resource constrained settings. In this paper, we draw on two sets of group discussions held among a group of approximately 15 HPSR researchers based in Nairobi, Kenya, who were conducting a range of embedded HPSR studies throughout the COVID-19 pandemic. The researchers, including many of the authors, were employed by the KEMRI-Wellcome Trust Research Programme (KWTRP), which is a long-standing multi-disciplinary partnership between the Kenya Medical Research Institute and the Wellcome Trust with a central goal of contributing to national and international health policy and practice. We share our findings in relation to three inter-related themes: 1) Ensuring the continued social value of our HPSR work in the face of changing priorities; 2) Responding to shifting ethical procedures and processes at institutional and national levels; and 3) Protecting our own and front-line colleagues' well-being, including clinical colleagues. Our experiences highlight that in navigating research work and responsibilities to colleagues, patients and participants through the pandemic, many embedded HPSR staff faced difficult emotional and ethical challenges, including heightened forms of moral distress, which may have been better prevented and supported. We draw on our findings and the wider literature to discuss considerations for funders and research leads with an eye to strengthening support for embedded HPSR staff, not only in crises such as the on-going COVID-19 pandemic, but also more generally.