This study investigates the impact of various machining conditions on the response variables, namely Tool Wear Rate (TWR), Material Removal Rate (MRR), and Hole Taper (HT), during rotary micro-Electrical Discharge Machining (mu-EDM) of Ti-6Al-4V plates with thicknesses of 0.5 mm (W1), 1 mm (W2), and 1.5 mm (W3). Implementing effective flushing techniques and consistent maintenance of machining conditions improved mu-EDM performance, particularly for high aspect ratios. Using a Taguchi-based L9 orthogonal array, experiments were designed and analyzed through Analysis of Variance (ANOVA). The study revealed that capacitance and electrode rotation speed (ERS) significantly contributed to MRR, with capacitance playing a more substantial role. Specifically, for the W3 workpiece, capacitance demonstrated a remarkable MRR of 0.01894 mm3 min-1, 51.12% and 63.10% greater than W1 and W2, respectively. Conversely, W1 exhibited the lowest TWR of 0.000193 mm3 min-1, 50.61% and 67.24% lower than W2 and W3. W1 also improved accuracy by significantly reducing HT compared to W2 and W3. Scanning Electron Microscopy (SEM) analysis explored the effects of voltage, capacitance, ERS, and workpiece thickness on micro-hole surfaces. SEM images revealed the presence of debris and burrs contributing to inaccuracies in micro-hole formation. Despite the challenges, the study emphasizes the importance of optimizing machining parameters for enhanced mu-EDM performance in challenging materials.