The Mecsekalja Zone is a strike-slip fault zone that plays an essential role in the structural framework of South Transdanubia. The metamorphic and deformation history of the crystalline basement of the Mecsekalja Zone has been determined thus far based exclusively on a few surface outcrops and near-surface samples. The Szentlőrinc-1 (Sztl-1) well penetrated the shear zone at a depth of approximately 2 km and brought drilling chips from a 220-m-long section of the basement to the surface. The aim of this study is to reconstruct the metamorphic and deformation history of the Mecsekalja Zone along the Sztl-1 well using these tiny samples. These drilling chips consist of single mineral and rock pieces that are dominated by quartz grains. This study concentrates on the detailed analysis of quartz grains utilizing the physical conditions of metamorphic evolution as well as ductile and brittle deformation to determine the chemical composition and rheology of quartz. The evolution of the studied area can be determined by evaluating analytical data measured by Raman spectroscopy, LA-ICP-MS, and FTIR spectroscopy. These data suggest that the maximum temperature of the early regional metamorphism was 500–575 °C, the temperature of the subsequent ductile deformation was below 500 °C including recrystallization occurred between 400 and 475 °C. During the structural evolution of the study area, two independent, single deformation events occurred. The earlier ductile deformation event was followed by a brittle event through the reactivation of the former ductile shear zone. Our model is in accordance with previous results concerning the evolution of the Mecsekalja Zone, thus, the shear zone, with an identical evolution, can be extended toward the southwest at least to the Sztl-1 well.