Over the past decade, several foodborne disease outbreaks provoked widespread reforms to the fresh produce industry. Subsequent concerns about wildlife vectors and contaminated manures created pressure on growers to discontinue use of manure-based composts and remove nearby semi-natural vegetation. Despite widespread adoption, impacts of these practices on ecosystem services such as pest control have not been assessed. We used a landscape-scale field experiment to quantify associations between compost applications, semi-natural vegetation, pest control services and lettuce yields on organic farms throughout California's Central Coast, a region experiencing food safety reforms. We found that farms with surrounding semi-natural vegetation supported a diverse arthropod assemblage, whereas a herbivore-dominated assemblage occupied farms in simplified landscapes. Moreover, predatory arthropods consumed more herbivores at sites with more surrounding non-crop vegetation and reduced aphid pest infestations in lettuce. Compost improved lettuce yields by increasing soil nutrients and organic matter, but affected neither pest control nor Escherichia coli prevalence. Synthesis and applications. Food safety concerns are prompting practices that simplify farms and landscapes. Our results demonstrate that two practices – elimination of manure-based composts and removal of non-crop vegetation – are likely having negative impacts on arthropod biodiversity, pest control and soil quality. Critically, our findings and previous research suggest that compost can be applied safely and that habitat removal is likely ineffective at mitigating food safety risk. There is thus scope for co-managing fresh produce fields for food safety, ecosystem services, and biodiversity through applying appropriately treated composts and stopping habitat removal.