Autotrophic hydrogen-oxidizing bacteria (HOB) have received increasing attention as a promising source of microbial protein (MP). However, most of the studies were conducted at relatively low ammonium concentrations (∼1 g N-NH4+/L). This study investigated the effect of high concentrations of ammonium and various nitrogen forms on the growth of Cupriavidus necator 335 for MP production. The cell growth was slightly inhibited at 2 g N-NH4+/L and was completely suppressed at 4 g N-NH4+/L. Inoculum from the early stage of exponential phase adapted better to the inhibition. Urea was the most preferred nitrogen source followed by nitrate and ammonium. Neither the ammonium concentration (within 2 g N/L) nor the different nitrogen sources altered the amino acid profiles significantly. This study demonstrated that waste streams containing high ammonium concentration (e.g., digestate) or with different forms of nitrogen (e.g., urine) could be used as a nitrogen source for MP production and thereby broadening the feedstocks and application of the process.