Cu-doped ZnO nanoparticles (NPs) were synthesised using Rubia cordifolia root extract and their photocatalytic degradation and antimicrobial properties were evaluated. Among all dopant concentrations, UV-VIS analysis of 5% Cu-ZnO NPs revealed a clean shift towards the visible range with a reduction in the band gap from 3.2 eV for pristine ZnO to 2.98 eV. Formed NPs were identified as wurtzite crystal structure (size of 16.67 nm) having a functional group of ZnO, using XRD and FTIR analysis. Highest photocatalytic degradation efficiencies of both Alizarine Red (AZ) (80%) and Rhodamine B (RhB) (82%) dyes were by 5% Cu-ZnO NPs. Statistical modelling and optimization were conducted using Response Surface Methodology (RSM) and Adaptive Neuro-Fuzzy Inference System (ANFIS), resulting in development of models having >90% predictive accuracy. Furthermore, the biogenic Cu-ZnO nanoparticles exhibits effective antimicrobial properties against both gram-positive (S. aureus) and gram-negative (E. coli) bacteria. The biogenic synthesis approach demonstrated enhanced photocatalytic efficiency and antimicrobial properties, suggesting its potential for environmentally friendly applications.