AimsThe purpose of this study was to evaluate the effect of warehouse storage conditions on the composition of the fungal community of green coffee beans (GCB) that were stored in jute sacks for 1year. Methods and ResultsMolecular characterization of the fungal community composition and population dynamics obtained by Q-PCR, CE-SSCP (Simpson's diversity index D) and Illumina MiSeq sequencing indicated that Saccharomycetales dominated during the first 6months of storage period with species as Meyerozyma guilliermondii and Pichia kluyveri. However, after 6months of storage, the filamentous genus Wallemia became dominant. Principal components analysis correlated this fungal dynamic with storage conditions and other variables as chromaticity (colour), water activity, moisture content, reducing sugars concentration, fungal infection and ochratoxin A production. ConclusionsThis study demonstrated that GCB stored in jute sacks after 6months of storage lead to fungal population dynamics, decreased chromaticity in GCB by bleaching and, then, affected overall quality. Significance and Impact of the StudyStorage plays an important role in the quality evolution during the handling of the GCB. In this context, the composition of the microbial community could be considered a marker to assess the trade value of the coffee beans.