Biodiversity loss in agricultural landscapes due to intensification of agriculture and degradation and loss of semi-natural habitats is a major issue that life cycle assessment (LCA) methods intend to address. No current LCA method is able to assess and compare impacts on the biodiversity of vegetable production systems as a function of farming practices and the local context. Based on a literature review and consultation with experts, the SALCA-BD expert system, originally designed to assess impacts on the biodiversity of cropland and grassland at field, rotation, and farm levels, was adapted to vegetable production systems. SALCA-BD is based on an inventory of the habitats found on a farm and a list of practices that can be implemented in these habitats. We distinguished an open field and a greenhouse as two distinct “level I” habitats, as a habitat’s openness favours the exchange of species with surrounding habitats. These two habitats were subdivided into “level II” habitats that corresponded to vegetable crops. Given the many types of vegetables, we used a clustering method to create a few categories that grouped vegetables that had similar potential to host biodiversity. We created a category for intercropped vegetables for fields in which multiple vegetables are grown at the same time, which is common on microfarms. We tested the expert system at field and farm levels using scenarios and a farm case study. We quantified effects of changes to individual practices and practice intensities at the field level on biodiversity. The results highlighted the importance of semi-natural habitats for preserving biodiversity, in addition to low-intensity practices, which indicates that assessment at the farm level is more informative than that at the field level. Because it considers habitats and practices in detail, SALCA-BD is useful for assessing biodiversity at field and farm levels and for comparing farming systems with the same land use and type of management (organic or conventional), which other LCA methods for assessing biodiversity cannot do. Field size, which is a driver of biodiversity, is considered indirectly only when semi-natural habitats are included. As SALCA-BD does not consider impacts of the background system, combining SALCA-BD with comprehensive methods for assessing impacts on biodiversity is a promising perspective for more complete assessment.