Legumes form a very important component in Malawi's cropping systems because of their roles in food security, income generation and soil fertility improvement through biological nitrogen fixation (BNF). They are commonly grown in various cropping systems including sole cropping, cereal-legume intercrops and legume-legume intercrops (also commonly referred to as "doubled-up"). However, information on BNF by the pigeon pea and cowpea under doubled-up system is scanty. Therefore, a study was conducted at two sites of Lilongwe and Dowa in the 2013/14 growing season, to quantify and compare the amounts of biologically fixed nitrogen in the three legume cropping systems. The experiments were laid out in a randomized complete block design and BNF was estimated using the modified nitrogen difference method. Results showed that there were significant differences (P < 0.05) in nodule numbers, nodule dry weights, and quantities of N 2 fixed per unit area due to cropping systems' effects at both sites. Sole cropped pigeon pea produced the highest N 2 fixed (92.9 kg N ha ) by 33%. From this study it can be noted that all three legume cropping systems can lead to substantial amounts of biologically fixed nitrogen, but their implementation should consider both combinations and environmental factors for specific sites.