Soil nutrient constraints coupled with erratic rainfall have led to poor crop yields and occasionally to crop failure in sole cropping in the Guinea savanna of West Africa. We explored different maize-grain legume diversification and intensification options that can contribute to mitigating risks of crop failure, increase crop productivity under different soil fertility levels, while improving soil fertility due to biological N2-fixation by the legume. There were four relay patterns with cowpea sown first and maize sown at least 2 weeks after sowing (WAS) cowpea; two relay patterns with maize sown first and cowpea sown at least 3 WAS maize in different spatial arrangements. These were compared with groundnut-maize, soybean–maize, fallow-maize and continuous maize rotations in fields high, medium and poor in fertility at a site each in the southern (SGS) and northern (NGS) Guinea savanna of northern Ghana. Legumes grown in the poorly fertile fields relied more on N2-fixation for growth leading to generally larger net N inputs to the soil. Crop yields declined with decreasing soil fertility and were larger in the SGS than in the NGS due to more favourable rainfall and soil fertility. Spatial arrangements of relay intercrops did not have any significant impact on maize and legume grain yields. Sowing maize first followed by a cowpea relay resulted in 0.18–0.26 t ha−1 reduction in cowpea grain yield relative to cowpea sown from the onset. Relaying maize into cowpea led to a 0.29–0.64 t ha−1 reduction in maize grain yield relative to maize sown from the onset in the SGS. In the NGS, a decline of 0.66 and 0.82 t ha−1 in maize grain yield relative to maize sown from the onset was observed due to less rainfall received by the relay maize. Groundnut and soybean induced 0.38–1.01 t ha−1 more grain yield of a subsequent maize relative to continuous maize, and 1.17–1.71 t ha−1 more yield relative to relay maize across both sites. Accumulated crop yields over both years suggest that sowing maize first followed by cowpea relay is a promising ecological intensification option besides the more common legume–maize rotation in the Guinea savanna, as it was comparable with soybean–maize rotation and more productive than the other treatments.