Nitrogenase is one of the most complex enzymes known to date. The extensively studied molybdenum nitrogenase consists of two protein components and three metal centers that are critical for nitrogenase activity. The inherent complexity of this enzyme system, which is further compounded by the sensitivity of the metal clusters toward oxygen, makes the large-scale purification of fully active nitrogenase proteins a formidable task. This chapter highlights several methods that have been developed for the purification of nitrogenase proteins over the past few decades. Techniques used include weak anion exchange chromatography, size exclusion chromatography, and immobilized metal affinity chromatography. These methods can be selectively applied to nitrogenase variants and other related proteins.