Commercialization of food crops, such as maize can dynamically shift control over productive resources or accrued income from women to men. This can restrict women’s ability to access or buy productive inputs. However, scanty information is available on how changing gender roles and relations can affect smallholder farmers’ use of sustainable intensification practices. This study described how gender inequalities in access to resources and appropriation of gains affect the uptake of sustainable intensification (SI) practices among maize commercializing farmers in eastern Uganda. Qualitative Survey data collected from a random sub-sample of 72 (36 women and 36 men) maize farmers from 584 maize commercializing smallholder farmers survey participants, was subjected to thematic content analysis. It was intended to follow up four unique profiles of farmers; those who did not use SI practices, the ones who used only intensification (improve maize varieties and fertilizers) or sustainable practices (organic manure and maize-legume intercrop), and those who used joint, one or more sustainable intensification practices. Findings revealed all four profiles to be highly gendered. Only women did not use any SI practice, and only men used intensification practices due to gender roles, responsibilities, and tasks shaped by traditions that give men terminal control over productive assets and gained resources. Both men and women used sustainable and sustainable intensification practices because of the negotiation process and opportunities that gave women more rights over resources. Thus, social-cultural histories and values constrain married women from implementing innovations such as SI practices because these values restrict women’s authority over productive resources. It is recommended that for inclusive transformative interventions to be introduced successfully in rigid patriarchal contexts, it is vital to enhance the negotiation skills of women.