Prior to the COVID-19 pandemic the fields of Science, Technology, Engineering, Maths and Medicine (STEMM) in Higher Education (HE) were beginning to tackle their lack of diversity. The COVID-19 pandemic has seen the HE sector (including universities, publishers and funding bodies) enter a period of upheaval that risks reversing such progress. This article demonstrates how the unequal impact of the COVID-19 pandemic on the professional and personal lives of groups currently under-represented in academic STEMM is likely to widen and reproduce systemic inequalities already present within these fields. Evidence emerging from the streamlined COVID-19 related funding call indicates a backward step in gender equity when compared to most recent UKRI figures. The lack of data on other protected characteristics makes understanding and mitigating the damage a significant challenge. We outline specific actions that must be taken to address this challenge, ultimately arguing that academic STEMM must use this time of change as an opportunity to embed policies and practices that place equality, diversity and inclusion at the forefront.