The importance of atomic structure to understand the superconducting β-Tungsten (W) thin films especially their critical transition temperature (Tc) and upper critical magnetic field Hc2(0) is reported. Here, Tc and Hc2(0) for a low thickness (~ 35 nm) film are found to be ~ 3.14 K and 10.72 T, whereas for a comparatively thicker (~ 60 nm) film, these are 1.38 K and 2.34 T, respectively. The β-phase is identified by grazing-incidence X-ray diffraction. The microstructure is probed by transmission electron microscopy, where high-resolution images manifest an improvement in crystallinity of the nanoscale grains in a disordered matrix with increasing film thickness. A drastic change in atomic structure corresponding to two different thicknesses is found to be associated with the change in oxygen concentration. Particularly, the existence of amorphous-W in the presence of β-W is revealed in 35 nm film, which is further supported by ab-initio calculations. Based on the atomic and microstructure, superconducting properties of the β-W films are analyzed and discussed. Graphical abstract: Correlation between the superconducting transition temperature and microstructure with varying β-tungsten film thickness [Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to The Materials Research Society.