Decline of return in maize monoculture requires amendment of nutrients removed from the soil through retention of biomass on the soil with some addition of inorganic fertilizers. This study was executed for three consecutive years (2013-2015)to evaluate the effect of pruning levels while leaving the upper (0, 2, 4 and 6) parts of perennial pigeon pea and N levels (18, 41, 64, 87 and 110 kg ha-1) on yields of component crops and on some soil nutrients in maize/pigeon pea intercropping. The result indicated that the main effects due to pruning of pigeon pea and incorporation in to the soil and N level were significant for maize biomass weight during 2013 and 2014 and for maize grain yield throughout the experimental periods. Pruning of lower branches of pigeon pea while leaving the upper 2 in maize/pigeon pea intercropping increased grain yield of maize by 8% compared to the sole maize monocropping and produced a mean pigeon pea grain yield of 972 kg ha-1. It also reduced soil acidity, increased soil organic carbon, total N and available P compared to the sole maize monoculture. The highest LER of 1.42 and the highest net benefit of Birr 32,347 ha-1 were also obtained due to pruning of pigeon pea while leaving the upper 2 and incorporating in to the soil in intercropping of maize/pigeon pea at reduced N level. This branch management at reduced N level is recommended for the high productivity and reduced resource use efficiency for sub-humid areas of Bako.