The use of catalytic membranes as microstructured reactors without a separative function has proved effective. High catalytic activity is possible with minimal mass transport resistances if the reactant mixture is pushed to flow through the pores of a membrane that has been impregnated with catalyst. In this study, n-heptane (C7H16) was hydrocracked and hydro-isomerized within a plug-flow zeolitic catalytic membrane-packed bed reactor. The metallic cobalt (Co) precursor at 3 wt.% was loaded onto support mesoporous materials MCM-48 to synthesize heterogeneous catalysis. The prepared MCM-48 was characterized by utilizing characterization techniques such as scanning electron microscopy (SEM), X-ray diffraction (XRD), energy dispersive X-ray analysis (EDAX), Fourier transform infrared (FTIR), nitrogen adsorption–desorption isotherms, and the Brunauer–Emmett–Teller (BET) surface area. The structural and textural characteristics of MCM-48 after encapsulation with Co were also investigated. The analyses were performed before and after metal loading. According to the results, the 3 wt.% Co/MCM-48 of metallic catalyst in a fixed bed membrane reactor (MR) appears to have an excellent catalytic activity of ~83% during converting C7H16 at 400 °C, whereas a maximum selectivity was approximately ~65% at 325 °C. According to our findings, the synthesized catalyst exhibits an acceptable selectivity to isomers with multiple branches, while making low aromatic components. In addition, a good catalytic stability was noticed for this catalyst over the reaction. Use of 3 wt.% Co/MCM-48 catalyst led to the highest isomerization selectivity as well as n-heptane conversion. Therefore, the heterogeneous catalysis MCM-48 is a promising option/ alternative for traditional hydrocracking and hydro-isomerization processes.