Leguminous‐based intercropping, combined with conservation agriculture, is a promising approach to improve soil fertility, crop yields, and sustainable land use for smallholder farmers in sub‐Saharan Africa, including Malawi. This study aimed to assess the effects of incorporating legume‐based intercropping systems involving pigeon pea (Cajanus cajan) and cowpea (Vigna unguiculata) into the deep bed farming (DBF) system promoted by Tiyeni in northern Malawi. The study used a split plot design with cropping systems (CS) as the main plots and tillage systems (TS) as the sub‐plots. All treatments were replicated three times. The study encompassed two cropping seasons, where CS included legume‐based treatments, sole cropped maize (Zea mays) without fertilizer (MZ) and sole cropped maize with 92 kg top dressing N fertilizer per hectare (MZ + 92), while TS included DBF and conventional tillage (CT). The study found that all plots with leguminous crops on both DBF and CT showed higher levels of ammonium (NH4+), nitrate (NO3−) and phosphorus (P) in the soil, but DBF had significantly higher levels over 2 years. Intercropping systems showed higher land productivity (land equivalent ratio > 1) than sole cropping in both years, indicating that legume‐based cropping can improve land use efficiency and yields. It can be noted from this study that intercropping systems based on cereals and legumes, implemented in DBF, has the potential to sustain agricultural intensification in sub‐Saharan African countries where access to chemical fertilizers is limited among smallholder farmers.