A growing body of work clearly documents the gendered inequalities in health. The COVID-19 pandemic further exposed these deep inequities: men appear to be more vulnerable to poorer outcomes, but most of the global health workforce is female who are at increased risk of exposure to hospital infection. However, researchers often fail to adequately embed gender as part of the public health research. This paper reports findings from a synthesis exercise that identified some of the challenges of integrating gender in the design and processes of research studies in four projects conducted in six low- and middle-income countries. Through a collective retrospective meta-synthesis process with researchers from each project, we identified two main themes; (i) we deep dive on two of the structural pillars of conducting public health research (design and process) and (ii) we describe some of the underlying opportunities and resistances to the integration of a gender perspective in these research projects. In conclusion, we suggest that public health funding bodies require researchers to integrate gender in public health research from early on as part of the design and to conduct gendered analysis, as part of the overall drive towards more equitable health systems delivery.