Mn-doped Co3O4 nanoparticles of 15 nm were developed via solvothermal synthesis. Mn@Co3O4 microspheres were developed via controlled annealing treatment at 600 °C. Mn@Co3O4 microspheres demonstrated an average diameter of 5.5 µm, with specific area (BET) of 73.7 m2 g−1. The pore diameter was centered at 13.1 nm, and the mean pore size was 16 nm; porous structure could secure extensive interfacial surface area. Mn@Co3O4 microspheres were integrated into ammonium perchlorate (AP) matrix. The catalytic activity of Mn@Co3O4 on AP decomposition was assessed via DSC and TGA/DTG. Whereas Mn@Co3O4/AP nanocomposite demonstrated decomposition enthalpy of 1560 J g−1, pure AP demonstrated 836 J g−1. While Mn@Co3O4/AP nanocomposite demonstrated one decomposition temperature at 310 °C,pure AP exposed two decomposition stages at 298 °C, and 453 °C. Decomposition kinetics was investigated via isoconversional (model free) and model fitting. Kissinger, Kissinger–Akahira–Sunose (KAS), integral isoconversional method of Ozawa, Flyn and Wall (FWO), and differential isoconversional method of Friedman. Mn@Co3O4/AP demonstrated apparent activation energy of 149.7 ± 2.54 kJ mol−1 compared with 173.16 ± 1.95 kJ mol−1 for pure AP. While AP demonstrated sophisticated decomposition models starting with F3 followed by A2, Mn@Co3O4/AP nanocomposite demonstrated A3 decomposition model. Mn@Co3O4 can expose active surface sites; surface oxygen could act as electron donor to electron deficient perchlorate group. Furthermore, Mn@Co3O4/AP could act as adsorbent of released NH3 gas with efficient combustion. This study shaded the light on Mn@Co3O4 as potential catalyst for AP decomposition.