Studies have often examined the effects of one dimension of work organization (WO) on the gender pay gap (GPG) by considering single contexts. However, research has rarely addressed how different factors of WO intersect to shape the GPG across contexts. This article fills this gap in the literature by comparing the chemical industry and financial services sectors in Spain. The article analyses how WO is formalized in collective bargaining and how regulations translate in practice at the company level. While different configurations of intertwining inequalities emerge in each context analysed, managerial discretion is a common key feature contributing to the GPG. Gaps in regulation allow unilateral recruitment, promotion and pay practices. Simultaneously, managerial practices distort or circumvent regulation by abusing or misusing certain concepts. The distance between regulation and practice is embedded in gendered organizational cultures and institutional inertia leading to gender inequalities in pay.