The novel applications of MoSi2 and SiC as matrix and reinforcing materials in the creation of high-performance composites were investigated in this work. In particular, Spark Erosion Machining's geometric tolerances were studied in order to shed light on the technique's potential for precision manufacture in the realm of MoSi2–SiC composites. Our research focused on evaluating critical parameters and their impact on machining performance, including material removal rate, surface roughness, wear rate and drilled hole accuracy. In-depth research revealed the critical input factors that had the greatest impact on the machining procedure. Notably, parameters such as current (32%), sparking on time (23%), sparking gap voltage (12%), dielectric pressure (12%), and sparking off time (17%) emerged as the most influential factors, as determined by ANOVA analysis. These findings provide valuable insights into optimizing the Sparking EDM approach for MoSi2–SiC composite materials. This study further demonstrated the improvement in composite desirability ratings across multiple performance criteria, highlighting the effectiveness of Sparking EDM in enhancing machining outcomes (e.g., from 0.8523 to 0.9527). Correlations between the EDM's output responses were found to be quite high when geometric tolerances and the coefficient of determination (R2) were used (0.7858, 0.9625, 0.8427, 0.8678, 0.8474, 0.8368, 0.8344, 0.8671). Consider that, for the sake of a more complete understanding of the procedure's approach, the emphasis is on the methodology rather than the multifaceted metal removal mechanisms involved. This research doesn't dive further into the physical concerns of Spark Erosion Machining, but it does provide insights into the practical application of this technique in the precision manufacturing of MoSi2–SiC composite materials. For real-world medical applications such implanted devices, dental implants, surgical instruments, biological sensors and diagnostics, this study provides a valuable and encouraging approach. A validation experiment verifies the results, proving the feasibility of improved spark erosion in high-precision production. The results of this research show that EDM methods can be fine-tuned to produce ceramic composites with much greater MRR, superior surface finishes and a marked decrease in subsurface cracking and microstructural modifications. This is essential for protecting the integrity of materials used in life-saving medical equipment.