Van der Waals single-layer materials are characterized by an inherent extremely low bending rigidity and therefore are prone to nanoscale structural modifications due to substrate interactions. Such interactions can induce excess charge concentration, conformational ripples, and residual mechanical strain. In this work, we employed spatially resolved Raman and photoluminescence (PL) images to investigate strain and doping inhomogeneities in a single layer exfoliated molybdenum disulphide crystal. We have found that correlations between the spectral parameters of the most prominent Raman bands A1′ and E′ enable us to decouple and quantify strain and charge doping effects. In comparison with Atomic Force Microscopy (AFM) topography, we show that the spatial distribution of the position of the A− -trion PL peak is strain sensitive and its linewidth can capture features smaller than the laser spot size. The presented optical analysis may have implications in the development of high-quality devices based on two-dimensional materials since structural and electronic modifications affect considerably their carrier mobility and conductivity.