Vegetables are commonly produced with high inputs of pesticides and fertilisers to boost production and meet cosmetic market standards. Yet, reports on the relationships between agrochemical inputs and crop productivity are scattered and an overview is missing. We assessed the relationship between pesticide and nutrient inputs and crop productivity for five vegetable crops in the south of Uruguay at field and farm level and explored the relation with farm resource endowment. We analysed crop yield and input use for tomato, onion, sweet potato, and strawberry with a dataset of 82 farms and 428 fields constructed between 2012 and 2017. Clear crop-specific patterns in pesticide and nutrient input levels were found, despite considerable variation across fields within the same crop. Strawberry and long cycle tomato had the greatest pesticide input regarding of the number of applications (20 and 18, respectively) and pesticide load (21 kg AI per ha). Cumulative nutrient inputs were greatest for long cycle tomato (1127 kg per ha). The relationships between inputs and yield were weak or non-significant, indicating inefficiencies and overuse of inputs, and there was no agronomical rationale for input use. We found substantial variation in management practices between fields and farms. In several cases, 21% of the fields and 17% of the farms producing onion, strawberry and tomato, attained relatively high yield levels with limited input levels. Yield and input use levels were not related to farm resource endowment. Our findings question the efficiency of the current high levels of pesticide and nutrient inputs in Uruguayan vegetable systems. The inputs may pose environmental and human health risks and in most cases did not increase yields. Learning from positive deviant farmers in combination with guided farm redesign, high-quality extension services, and use of context-specific knowledge and technologies may equip farmers to use more sustainable management practices.