From the perspective of environmental protection, the highly efficient degradation of antibiotics and organic dyes in wastewater needs to be tackled as soon as possible. In this study, an ecofriendly and green cube-shaped cobalt-doped zinc oxide nanoparticles (Co–ZnO NPs) photocatalyst using Pterocladia Capillacea (P. Capillacea) water extract loaded with 5, 10, and 15% cobalt ions were formed via co-precipitation process to degrade antibiotics. The prepared Co–ZnO NPs were tested as a photocatalyst for the photodegradation of ciprofloxacin (CIPF) in the presence of a visible LED-light source. Co–ZnO NPs have been obtained through the co-precipitation method in the presence of P. Capillacea extract as a green capping agent and reducing agent, for the first time. Several characterization techniques including FTIR, XRD, BET, XPS, TEM, EDX, SEM, TGA and DRS UV–Vis spectroscopy were applied to study the prepared Co–ZnO NPs. XRD results suggested that the average size of these NPs ranged between 42.82 and 46.02 nm with a hexagonal wurtzite structure. Tauc plot shows that the optical energy bandgap of ZnO NPs (3.19 eV) gradually decreases to 2.92 eV by Co doping. Examinations showed that 5% Co–ZnO NPs was the highest efficient catalyst for the CIPF photodegradation when compared with ZnO NPs and other 10 and 15% Co–ZnO NPs. A 10 mg/L solution of CIPF was photo-degraded (100%) within the first 15 min irradiation. The kinetics showed that the first-order model is suitable for displaying the rate of reaction and amount of CIPF elimination with R² = 0.952. Moreover, central composite design optimization of the 5% Co-doped ZnO NPs was also investigated.