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Grapevine decline is a top concern in viticulture worldwide and is often associated with many biotic and abiotic factors. Grape trunk diseases and viruses are some of the most frequently identified causes of vine dieback. However, a decline is sometimes observed when no mineral deficiency or excess, or pathogenic causes can be identified. Soil enzymatic and microbial activities are relevant bio-indicators since they are known to influence vine health. Grapevine associated microbiota, linked to vine fitness, is known to be influenced by soil microbiota coming from the microbial pool inhabiting the vineyard. This work describes the microbial diversity and activity of four different vineyard plots of the Bordeaux region, selected due to the presence of localised declining areas unexplained yet by disease symptoms. Soils were sampled in declining areas and areas within the same plot showing no decline symptoms, during autumn and spring periods. Significant differences in enzymatic activities, microbial biomass and activity were found among soils even if those soils presented quite similar physicochemical characteristics that could not explain these observed declines. The results of enzymatic assays distinguished patterns in autumn and spring periods with an overall greater enzymatic activity in soils from non-declining areas. This work suggests that soils displaying decline symptoms present a dysbiosis in functionality and diversity which is linked to vine health.