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The phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 shows biocontrol potential against Streptomyces scabies, which causes common scab of potato. To better characterize the impact of inoculating this specific biocontrol agent under field conditions, the microbiomes of the rhizosphere and the geocaulosphere of potato plants were characterized using next-generation sequencing. A single initial application or biweekly applications of LBUM223 were performed up to 11 weeks after planting. Rhizosphere and geocaulosphere soils (when potato tubers were produced) were sampled every 2 weeks. Following soil DNA extractions, 16S rRNA gene amplification and sequencing were performed using the Illumina MiSeq technology. The QIIME pipeline was used for data analyses. Results were generated from 45 rhizosphere and 27 geocaulosphere samples, for which 63,502 and 44,469 different operational taxonomical units were observed. Diversity comparisons between both datasets were performed. To our knowledge, this is the first time that the geocaulosphere microbiome is characterized and compared with the rhizosphere microbiome following inoculation with a specific microorganism. Eleven phyla accounted for 95% of the diversity, with Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria being the most abundant ones. Overall, the results obtained suggest that P. fluorescens strain LBUM223 does not significantly alter the autochthonous rhizosphere nor geocaulosphere microbiomes.