This sequence dataset (FASTQ format) was obtained by metabarcoding foliar fungal communities in conventional and organic vineyards. The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pair and sequenced on an Illumina MiSeq platform (v3 chemistry, 2x250 bp). In total, 120 leaves, corresponding to 1 leaf × 20 vines × 3 plots × 2 cropping systems (B for organic and I for conventional), were collected and sequenced. The samples were labelled as follow: [Vine number]-[Cropping System Code][Plot number]*.fastq. The 240 files correspond to the forward (R1) and reverse (R2) sequences of each sample. Two samples were negative controls of the extraction and PCR steps: Ctrl-ex and Blc-PCR. Six PCR products were sequenced twice independently to serve as technical replicates for sequencing. The name of those samples start with "Rep". This dataset was used to compare the effect of the cropping system on fungal community and network α- and β-properties (Pauvert et al. Microbial networks inferred from metabarcoding data lack replicability: consequences for next-generation biomonitoring, submitted).