Background: Previous studies have found the prevalence of lameness in working horses to be 90-100%. Risk factors for lameness in this important equine population, together with risk-reduction strategies adopted by their owners, are poorly understood. The objective was to uncover risk factors for lameness and limb abnormalities in working horses, by associating clinical lameness examination findings on three occasions over two years with owner reported changes in equine management and work practices over this period. Methodology/Principal Findings: Twenty-one communities of horse owners in Jaipur, India, took part in a participatory intervention (PI) project aiming to reduce risk factors for poor welfare, particularly lameness and limb problems. Associations between quantitative measures of equine lameness/limb abnormalities and reported changes in management and work practices were compared with 21 control (C) communities of owners where no intervention had taken place. Key findings from 'complete cases', where the same horse stayed with the same owner for the whole study period (PI group = 73 owners of 83 horses, C group = 58 owners of 66 horses), were that more positive statements of change in equine management and work practices were made by PI group owners than C group owners. A mixed picture of potential risk factors emerged: some reported management improvements, for example reducing the weight of the load for cart animals, were associated with improved limbs and lameness, and others, such as making improvements in shoeing and increasing the age at which their animals started work, with negative outcomes. Conclusions/Significance: This study illustrates the complexity and interacting nature of risk factors for lameness in working horses, and highlights the importance of longitudinal investigations that recognise and address this. PI group owners found the project useful and requested similar inputs in future. Our findings demonstrate the value of exploratory and participatory research methodology in the field of working horse welfare.