This work focuses on the joining of Inconel-625/SS-304 using selective microwave hybrid heating (SMHH) technique. Input power, filler powder particle size, separator, and susceptor size are considered for experimentation according to the Definitive Screening Design. The multi-objectives measured are UTS, FS, and microhardness. XRD results show the intermetallic/secondary phases, and FESEM micrographs show the metallurgical bonding occurs between base metal and filler. The joint and interface region had an average microhardness of 204 ± 10 HV and 342 ± 18 HV, respectively. The UTS and FS of the weldments measured to 550 MPa and 805 MPa. MOJAYA technique is utilized for multi-objective optimization, and R-method determined the optimal process parameters. The optimal process parameters found to 2.2 kW, 25 μm powder, 120 grit and 0.804 mm separator. The confirmation test reveals UTS − 566 MPa, FS − 903 MPa, and microhardness − 365 HV, which closely matched with predicted observations.