Herein, we report, for the first time, the reduction reaction kinetics of ciprofloxacin organic molecules based on structural and micromorphological conditions of an electrocatalytic system of Bi0.5Na0.5Ba(TiO3)2 (BNT-BT) thin films. XRD analysis showed the coexistence of rhombohedral and tetragonal structures for the BNT-BT thin films annealed at 600, 650, and 700 °C, showing that the first one had a greater number of surface defects, which Raman spectroscopy confirmed. Analysis of the 3D micromorphological evaluation showed that an annealing temperature increase from 600 to 700 °C does not induce significant changes in the topographical profile. However, BNT-BT thin films annealed at 600 °C displayed more anisotropic surface microtexture, high spatial complexity, and low spatial frequencies. For the reactive surface of BNT-BT films, the electroanalytical assays showed that electrons from the conduction band are captured by oxygen adsorbed on the film surface, forming superoxide radicals that attack ciprofloxacin molecules, promoting their degradation. The best performance observed for the BNT-BT thin films annealed at 600 °C is attributed to their unique structural and micromorphological properties compared to the films annealed at higher temperatures. Our results prove that the proposed thin film deposition process is promising for developing new electrocatalytic devices.