Nata de coco, chemically known as bacterial cellulose (BC), is mostly manufactured in Southeast Asian countries and Hainan, China. Failures happened frequently due to the open fermentation system of nata de coco, especially in winter and spring. This study investigated the differences between normal and abnormal fermentation processes in a nata de coco manufacturing factory. Results revealed significant variations in microbial composition and metabolite profiles between abnormal and normal fermentation batches. Lactiplantibacillus plantarum GPb4103 was further isolated and screened from the abnormal fermentation broth to investigate its potential inhibitory effect on BC synthesis of Komagataeibacter nataicola JY6211. Although co-culturing the strain JY6211 and L. plantarum GPb4103 resulted in synergistic growth, BC yield decreased by up to 53%. The KEGG pathway analysis of differential metabolites showed that the GPb4103 hindered BC synthesis of the JY6211 by altering accumulation of metabolites in the fermentation broth through metabolic pathways. This study provides new insights into how specific microbes could affect BC synthesis of K. nataicola during nata de coco production, thereby illuminating challenges faced in commercial BC production, such as inconsistent products quality and problematic production processes.