This study developed a novel pH-mediated antimicrobial dyeing process of cotton with prodigiosins nanomicelles produced by microbial fermentation. The average diameter of the pigment nanomicelles was 223.8 nm (range of 92.4–510.2 nm), and the pigment concentration was 76.46 mg/L. It was found that the superior dyeing effect of cotton fabric was achieved by adjusting the dye bath pH. When the pH was three, dyed cotton under 90 °C for 60 min exhibited the greatest color strength with good rubbing, washing and perspiration color fastness. By the breaking strength test and XRD analysis, it was concluded that the cotton dyed under the optimum condition almost suffered no damage. In addition, due to the presence of prodigiosins, dyed cotton fabric under the optimal process showed outstanding bacteriostatic rates of 99.2% and 85.5% against Staphylococcus aureus and Escherichia coli, respectively. This research provided an eco-friendly and widely-applicable approach for antimicrobial intracellular pigments with the property of pH-sensitive solubility in water to endow cellulose fabric with color and antibacterial activity.