The joining of austenitic stainless steels through microwave hybrid heating has gained much attention due to its advantages, like uniform and volumetric heating. However, to establish a microwave joining process for promising applications, a microstructural study of the welded joint is still an area to explore. In the present study, microstructural analysis of austenitic stainless steel (SS304) joints is explained through optical microscopy, scanning electron microscopy (SEM), elemental mapping, X-ray diffraction (XRD) and Vickers' micro-hardness tester. Further, detailed microstructural analysis of interlayer and heat-affected zone (HAZ) is studied through electron back-scattered diffraction (EBSD). XRD results reveal the development of various Ni, Cr and the M23C6 type carbides at the joint interlayer region. SEM results point toward non-epitaxial grain evolution along the fusion zone. The mean microhardness of 350 ± 20 HV was determined at the joint interlayer region. A relatively fine grain structure was observed along the fusion boundary. However, moving away from the joint, two different forms of coarse grain heat-affected zone (CGHAZ) were observed. The presence of two different forms of CGHAZ is confirmed through inverse pole figure maps and grain size plots. The presence of high-angle boundaries (HABs) at 60° rotation describes the twin boundaries characterized along the <111> axis. The existence of improved fractions of HABs in the microwave-joined specimen of SS will favor the microstructure to retard bulk deformation. The joint specimen endures a maximum force of 6.98 kN, and the ultimate tensile strength of 613 MPa with 4.75% of elongation. It is observed that microhardness observations and the microstructural studies in the research help establish a solid microstructure-property correlation for the joined material.