Cotton is essentially a smallholder crop across tropical countries. Being a major cash crop, it plays a decisive role in the livelihoods of cotton-producing farmers. Both conventional and organic production systems offer alternative yet interesting propositions to cotton farmers. This study was conducted in Nimar valley, a prominent cotton-producing region of central India, with the aim of categorically evaluating the contribution of management and fixed factors to productivity on conventional and organic cotton farms. A study framework was developed considering the fixed factors, which cannot be altered within reasonable limits of time, capacity and resources, e.g., landholding or years of age and/or practice; and management factors, which can be altered/influenced within a reasonable time by training, practice and implementation. Using this framework, a structured survey of conventional and organic farms operating under comparable circumstances was conducted. Landholding and soil types were significant contributors/predictors of yield on organic farms. In contrast, landholding was not the main factor related to yields on conventional farms, which produced the highest yields when led by farmers with more than five years of formal education and living in a joint family. Nitrogen application, the source of irrigation (related to timely and adequate supply), crop rotation and variables related to adequate plant population (seed source, germination rate and plant thinning) were the main management factors limiting cotton yields among conventional and organic farms. Both organic and conventional farms in the Nimar valley exhibited a similar pattern of variation in cotton yields and technical efficiency. This study highlights the enormous scope for improving cotton productivity in the region by improving technical efficiency, strengthening extension services and making appropriate policy interventions.