Nitrogen (N) is the most critical plant nutrient. Maize has a high nitrogen demand. Low maize (Zea mays L.), yields in smallholder farms of Malawi, the country’s staple, is attributable to declining N fertility aggravated by the ever increasing price of fertilizer. Little effort has been made to establish the best nitrogen rate in a maizecowpea and maize-bean intercrop under variable soil conditions as a way of improving production, and was the objective of the current study. Field experiments were conducted at Chitedze Agricultural Research Station in Lilongwe and Makoka Agricultural Research Station in Zomba during the 2016/17 growing season. A split plot layout in a randomized complete block design, with three replicates was used. The main plots were; sole maize, sole bean, sole cowpea, bean/maize and cowpea/maize intercrop systems. The sub plots were N fertilizer rates (0, 52.5, 78.75 and 105 kg N ha-1 ), applied as urea. The data collected was subjected to analysis of variance using SAS software version 9.3 (SAS Institute Inc.) at P<0.05. Means were separated using Duncan Multiple Range (DMRT) test at 95% significance level. The results showed that application of N increased maize N uptake and grain yield. NUE however decreased with increasing N fertilizer rate.