Gender equality work in organisations has been criticised for weak results and an unclear political agenda. Studies on such work that put emotions at the centre are rare. The aim of this article is to examine the relationship between feelings of discomfort and practical gender equality work in companies, in projects which are facilitated by external gender experts in collaboration with company employees. Interviews and project documents from four companies involved in a regional gender equality project in Sweden form the empirical basis. Findings show that there was an aspiration to feel discomfort about inequality, among both gender experts and company employees, which was also embedded in recurring practice aiming for feeling and interpreting inequality. The discomfort among interviewees can be understood as signalling both authentic engagement and progress, but may also clash with specific organisational emotion norms and lead to problems associated with individualising responsibility. The article shows the import of discomfort and related emotions in gender equality work, and can be used for critical reflections on and realignment of ideas that inform these efforts.