Organic-inorganic metal halide perovskites (MHPs) have recently been receiving a lot of attention due to their newfound application in optoelectronic devices, including perovskite solar cells (PSCs) which has reached power conversion efficiencies as high as 25.5%. However, the fundamental mechanisms in PSCs, including the correlation of degradation with the excellent optoelectrical properties of the perovskite absorbers, are poorly understood. In this paper, we have explored synchrotron-based soft X-ray characterization as an effective technique for the compositional analysis of MHP thin films. Most synchrotron-based studies used for investigating MHP so far are based on hard X-rays (5–10 keV) which includes various absorption edges (Pb L-edge, I L-edge, Br K-edge, etc.) but are not suited for the analysis of the organic component in MHPs. In order to be sensitive to a maximum number of elements, we have employed soft X-ray-based scanning transmission X-ray microscopy (STXM) as a spectro-microscopy technique for the characterization of MHPs. We examined its sensitivity to iodine and organic components, aging, or oxidation by-products in MHPs to make sure that our suggested method is suitable for studying MHPs. Furthermore, methylammonium triiodide with different deposition ratios of PbI$_2$ and CH$_3$ NH$_3$ I (MAI), and different thicknesses, were characterized for chemical inhomogeneity at the nanoscale by STXM. Through these measurements, we demonstrate that STXM is very sensitive to MHP chemical composition and homogeneity. Thus, we highlight the utility of STXM for an in-depth analysis of physical and chemical phenomena in PSCs.