Microwave heated reactor which was loaded with carbon fiber supported iron and molybdenum incorporated monometallic catalysts was used to produce COx free hydrogen from ammonia. Impregnation procedure was applied to synthesize the catalysts at different metal loading (4-14 wt % according to ICP-OES) using iron nitrate or ammonium molybdate and reaction tests were carried out under the flow of pure ammonia (GHSV: 36,000 ml/hg(cat)). Activities of molybdenum incorporated carbon fiber catalyts are found to be lower than that of the iron loaded ones in the conventional reaction system. The effect of metal loading was clealy seen in the activity of molybdenum incorporated catalyst, unlike iron incorporated catalyts, especially under high reaction temperature conditions. Catalysts showed greatly enhanced activities in microwave heated system in comparison to conventionally heated reactor system. Complete conversion of ammonia was achieved at 500 degrees C by using molybdenum incorporated catalysts and at 450 degrees C by using iron incorporated catalysts (with GHSV of 36,000 ml/hgcat) in microwave heated reactor system. Transfer of energy directly to the active species and formation of carbide species, Fe2C or Mo2C, during the reaction under microwave application could be considered as the major factors leading to a better ammonia conversion. Structural properties of carbon support materials, such as the surface area, could be effective on the activity of the catalysts via the distribution of active species, however, this would be more pronounced effect in conventional system.