Catch-neuter-vaccinate-release (CNVR) programmes for free-roaming dogs (FRD) are humane and effective in controlling dog populations in developing countries. However, each component, from capture to release, can impact an individual animal’s welfare. This study aimed to develop a standardised welfare assessment scoring system for evaluating the welfare of dogs undergoing routine CNVR procedures at a veterinary training facility in Goa, India and to assess the impact of a targeted staff training intervention by comparing welfare assessment scores before and after its implementation. A score-based protocol was designed, incorporating 22 animal-, resource-, and management-based parameters covering six key steps of the CNVR procedure: catching/transport; cage/holding area; pre-operative period; surgery; post-operative period; and release. Eighty-two dogs were assessed initially. Areas for improvement were identified and informed the design of a targeted staff training intervention involving theory-based lectures and interactive sessions. Knowledge was assessed before and after receiving the intervention, with total scores on the assessment improving. The welfare assessment was repeated on another 81 dogs. Total welfare scores for individual dogs improved significantly after the staff intervention compared with before. This study demonstrates that a welfare assessment tool can be used to assess the welfare of individual dogs in a busy CNVR programme; furthermore, it can inform the compilation and delivery of a targeted staff training intervention and demonstrate improvements in dog welfare after such an intervention.