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The development of high-performance photocatalysts is vital for combating water pollution and microbial contamination. In this study, visible-light-active Z-scheme heterojunction nanocomposites composed of Co3O4 and Nb2O5 (CNNC) were synthesized via co-crystallization and subsequent high-pressure annealing to enhance photocatalytic and antimicrobial performance. Structural and optical analyses via XRD, FESEM, TEM, XPS, and PL confirmed the heterojunction formation between porous Co3O4 nanoparticles (CONP) and columnar orthorhombic Nb2O5 nanoparticles (NONP). The CNNC exhibited significantly improved photocatalytic activity, achieving degradation efficiencies of 95.1% for methylene blue, 72.6% for tetracycline, and 90.0% for Congo red within 150 min. Kinetic studies showed that CNNC’s rate constants were 367% and 466% of those of CONP and NONP, respectively. Moreover, CNNC demonstrated a strong antibacterial effect on Staphylococcus aureus and Escherichia coli with ZOI values of 9.3 mm and 6.8 mm, respectively. Mechanistic analysis revealed that the Z-scheme charge-transfer pathway improved charge separation and reduced electron–hole recombination, contributing to the promoted photocatalytic efficiency. The nanocomposite also showed robust stability and recyclability over five times. These results highlight the promise of CNNC as a bifunctional, visible-light-driven photocatalyst for pollutant decomposition and microbial control.