- Labour is the single largest cost contributor and main limiting factor to development of the agricultural industry. Manual labour remains a major, essential factor for greenhouse-grown specialty crops. Furthermore, musculoskeletal injuries are prevalent during manual work processes performed in agricultural environments. This study aims to improve work efficiency and productivity and to identify tasks that can cause musculoskeletal injury. Working procedures were characterised using a work-study method, environmental conditions were recorded and a biomechanical analysis of the inspected task was conducted. An innovative measuring system was developed that enables synchronisation and analysis of the manufacturing, biomechanics, workload and environmental data. The study focused on the trellising and harvesting stages of pepper and tomato in greenhouses on two farms located in southwest Israel. We further conducted several experiments in which we changed the working method and assessed the effect on productivity. Another experiment was conducted to test the effect of three different trellising angles (30°, 60°, 90°) on labour and yield in tomato. The results revealed that in tomato, in comparison to current methods, picking 4 fruit per cycle will increase production rate by 17%, leaf removal from the fruit area will increase production rate by 14.4%—up to 40.2%—and the best trellising angle with respect to yield and labour will be 30°. Analysis of biomechanical risk showed that the maximum weight of lifted boxes should not exceed 12 kg, and when picking fruit growing low to the ground, the workers are exposed to medium to high risk of injury.