<p>Mediterranean agricultural systems, such as rainfed crops, are vital habitats for a distinctive arable flora, including endemic and threatened species. Over recent decades, their area declined dramatically due to the large-scale expansion of intensive agriculture. Nowadays, traditional olive groves that persist in several areas of Mediterranean region, a biodiversity hotspot, may act as refuges for arable plant communities. Still, their current suitability to support arable plant diversity remains under-characterized. This study aimed to evaluate the conservation value of remnants of traditional olive groves (<i>n</i> = 90 plots) in southern Portugal by applying quantitative criteria to score plant species and communities. Species were scored based on rarity (Rabinowitz approach) and vulnerability to extinction (Red List assessments). The conservation value of the community in each plot was calculated with a novel formula, based on a weighted sum of the species values. Weights were defined so that results were bounded within a fixed scale, yet incorporating the contribution of all species. The relationship between conservation value and dissimilarities in species composition was tested in relation to management practices (ploughing, cultivation, grazing, unmanaged), and indicator species for high- and low-conservation value communities were identified. The conservation value was highest in shallow ploughed olive groves and lowest in grazed ones. The indicator species identified can serve as monitoring targets of the conservation status of these habitats and as early warnings of compositional changes. Our approach provides a standardized and generalizable methodology to rank species and sites for prioritizing the conservation of these high-value habitats and plant species.</p>