Fischer-Tropsch synthesis combined with product workup is a promising route toward synthetic aviation fuel from renewable hydrogen and carbon sources like biomass, CO2, and waste. Cost savings can be achieved by reducing the number of gas treatment steps in new plants, but the consequence of contaminants in the feed needs investigation. While feeding 2.6 ppmV ammonia to a Fischer-Tropsch reactor, it was shown that ammonia was predominantly chemically converted into organic amines, with most nitrogen found in the water phase (89%), followed by heavy wax (7%) and light wax (1%). The concentration difference between water and light wax was shown to be due to the post-condensation separation of amines on polarity. Amines up to a chain length of 120 were detected in the heavy wax with MALDI-FT-ICR-MS, which, in combination with the high nitrogen content, suggests that amines have a similar chain growth probability compared to the main hydrocarbon products. Detailed product analysis with three independent analytical techniques showed that tertiary N,N-dimethylalkylamines were by far the most abundant amine class. This suggests that ammonia is decomposed on the cobalt surface and, potentially as a dimethylamine fragment, incorporated in the growing chain. Further evidence was obtained from the abundance of trimethylamine and from the reconciled nitrogen product analysis up to C100, which showed that the amine product distribution followed from naphtha onward the same ASF kinetics as alkanes and oxygenates while being distinctively different from the alkene distribution. The presented findings provide further avenues for studies of the Fischer-Tropsch reaction mechanism and indicate the opportunity of cost saving on gas treatment, while further validation is required to assess the impact on hydrocracking and product quality.