The machining of quartz due to hard, non-conducting and brittle behavior with desired accuracy and precision is always a challenge. Quartz is widely used in MEMS/MOEMS applications. However, wire electrochemical discharge machining (WECDM) has great potential to machine hard and brittle materials like quartz, glass FRP, etc. The WECDM process is a hybrid non-conventional manufacturing process which combines characteristics of electrochemical machining (ECM) and wire-electrical discharge machining (W-EDM). The present study discusses the investigation of the effect of the governing process parameters such as voltage, electrolyte concentration, and wire speed (feed) on material removal rate (MRR) and surface roughness (Ra) during the micro-machining of quartz using self-developed tabletop desktop WECDM setup. The hybrid methodology of Taguchi orthogonal arrays and Analysis of variance (ANOVA) is used to find the optimum parameters and their significant contribution to response parameters respectively. Experimental results reveal that a better surface finish and high material removal rate was obtained by zinc layered brass wire (150 μm diameter). The machining of quartz under the zinc layered brass wire can indeed enhance the surface quality characteristics and material removal rate. Also, the mathematical models were established in order to derive the relationship between input and response parameters which was successfully validated by the confirmation experiment. Furthermore, the machining quality observed by a Scanning electron microscope (SEM), reveals the presence shallow cracks at higher-end input parameters.