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Understanding the response of biodiversity to management, land use and climate change is a major challenge in farmland to halt the decline of biodiversity. Farmlands shelter a wide variety of taxa, which vary in their life cycle and habitat niches. Consequently, monitoring biodiversity from sessile annual plants to migratory birds requires dedicated protocols. In this article, we describe the protocols applied in a long-term research platform, the LTSER Zone Atelier “Plaine & Val de Sèvre” (for a full description see Bretagnolle et al. (2018) [1]). We present the data in the form of the description of monitoring protocols, which has evolved through time for arable weeds, grassland plants, ground beetles, spiders, grasshoppers, wild bees, hoverflies, butterflies, small mammals, and farmland birds (passerines, owls and various flagship species).