This research program investigated the total nitrogen removal capabilities of two pre-denitrification systems treating methanogenic municipal landfill leachate. During the startup phase, which is the focus of this paper, the ammonia concentration of the leachate was artificially and incrementally increased from about 200 mg N/L (“base”) to 1200 mg N/L (“target”) to simulate higher strength wastes. The initial attempt to reach the target ammonia concentration resulted in the accumulation of ammonia in both systems, with eventual nitrification failure. The second attempt was successful, with the only difference in procedures being the rate at which an external carbon source (methanol) was added to support anoxic denitrification. Preliminary data obtained from both systems, during the startup phase, indicated that the addition of external carbon to the anoxic reactor could significantly affect system performance during initial startup and operation. Firstly, the simultaneous increase in carbon loading with ammonia loading, to enable high rates of anoxic denitrification, was found to result in greater heterotrophic assimilation of ammonia in the anoxic reactor (i.e. 30% vs 10%) compared to the case when carbon loadings were not increased to match NOx production. The higher rate of anoxic ammonia assimilation, during the second attempt, was sufficient to supplement nitrification ammonia removal and prevent the accumulation of ammonia within the systems. Secondly, during the first attempt, it was found that increasing anoxic carbon loadings, after ammonia had accumulated in the systems, with the intent of increasing denitrification and assimilating excess ammonia, ultimately resulted in complete failure of nitrification. The increased denitrification returned additional alkalinity to the systems and resulted in reactor pH levels increasing by about 1 pH unit. The increase in pH raised the “free” ammonia fraction, of “total” ammonia, by almost an order of magnitude. It is believed that increases in aerobic “free” ammonia levels, resulting from the existing “total” ammonia levels and the increased pH, caused the nitrification failure.