The effect of ammonia in syngas on the Fischer–Tropsch synthesis (FTS) reaction over 100Fe/5.1Si/2.0Cu/3.0K catalyst was studied at 220–270°C and 1.3MPa using a 1-L slurry phase reactor. The ammonia added in syngas originated from adding ammonia gas, ammonium hydroxide solution, or ammonium nitrate (AN) solution. A wide range of ammonia concentrations (i.e., 0.1–400ppm) was examined for several hundred hours. The Fe catalysts withdrawn at different times (i.e., after activation by carburization in CO, before and after co-feeding contaminants, and at the end of run) were characterized by ICP-OES, XRD, Mössbauer spectroscopy, and synchrotron methods (e.g., XANES, EXAFS) in order to explore possible changes in the chemical structure and phases of the Fe catalyst with time; in this way, the deactivation mechanism of the Fe catalyst by poisoning could be assessed. Adding up to 200ppmw (wt. NH3/av. Wt. feed) ammonia in syngas did not significantly deactivate the Fe catalyst or alter selectivities toward CH4, C5+, CO2, C4-olefin, and 1-C4 olefin, but increasing the ammonia level (in the AN form) to 400ppm rapidly deactivated the Fe catalyst and simultaneously changed the product selectivities. The results of ICP-OES, XRD, and Mössbauer spectroscopy did not display any evidence for the retention of a nitrogen-containing compound on the used catalyst that could explain the deactivation (e.g., adsorption, site blocking). Instead, Mössbauer spectroscopy results revealed that a significant fraction of iron carbides transformed into iron magnetite during co-feeding high concentrations of AN, suggesting that oxidation of iron carbides occurred and served as a major deactivation path in that case. Oxidation of χ-Fe5C2 to magnetite during co-feeding high concentrations of AN was further confirmed by XRD analysis and by the application of synchrotron methods (e.g., XANES, EXAFS). It is postulated that AN oxidized χ-Fe5C2 during FTS via its thermal dissociation product, HNO3. This conclusion is further supported by reaction tests with co-feeding of similar concentrations of HNO3. Additional oxidation routes of iron carbide to magnetite by HNO3 and/or by its thermal decomposition products are also considered: Fe5C2+NOx (and/or HNO3)→Fe3O4. In this study, ion chromatography detected that 50–80% HNO3 directly added or dissociated from AN eventually converted to ammonia during or after its oxidation of iron carbide, resulting from the reduction of NOx (NOx+H2+CO→NH3+CO2+N2+H2O) by H2 and/or CO.