Conservation agriculture (CA), as a key component of sustainable intensification, has been widely promoted across sub-Saharan Africa (SSA) to address low crop productivity. However, the focus has mainly been on improving cereal grain yields, with less focus to its impact on nutritional outcomes. This study sought to assess the productivity potential of CA crop diversification systems and associated crop establishment techniques in terms of grain, protein, and energy yields. An on-station trial was implemented in Malawi for four cropping seasons (2014/15 to 2017/18). Four crop establishment techniques (ridge and furrow, jab planter, dibble sticks, and CA basins) were tested, while cropping systems included conventional cropping system (Conv), CA sole cropping (CaSole), CA intercropping (CA-intercropping), and CA rotations (CA-rotation). In 2014/15 and 2015/16 cropping seasons, characterised by medium and low rainfall, respectively, planting basins and ridge-furrow systems produced higher maize yields compared to jab planter and dibble stick systems. In 2015/16, big and small basins yielded 5061 and 3969 kg ha–1, while jab planter and dibble stick yielded 3476 and 3213 kg ha–1. When there was high and persistent rainfall (2016/17 and 2017/18), direct seeding (jab planter and dibble stick) outperformed basins and ridge-furrow systems. Therefore, the choice of planting basin sizes and whether or not to use dibble stick and jab planter needs to be guided by location or site-specific seasonal forecasts for best results. Grain yield in maize-legume rotation systems consistently outperformed other systems, with maize-groundnut rotations surpassing maize-cowpea intercrops by 987–2700 kg ha–1 over four cropping seasons. In intercropping systems, maize-pigeon pea outperformed maize-cowpea by 4–45% during the same period, while maize-cowpea rotation consistently out yielded maize-cowpea intercropping. Intercropping systems, however, provided substantial protein benefits, with maize-pigeon yielding +9.5% (2015/2016), +29.1% (2016/2017) over CA sole, and +2.2% (2017/2018) over cowpea intercropping. Sole systems (conventional and CA sole) yielded the highest caloric energy, while maize-cowpea rotation consistently reduced energy yield by 35% to 54% compared to the highest-yielding systems. Overall intercropping systems can outperform rotation systems in nutritional security but when focus is on maize grain yield alone, intercropping may reduce maize yield when compared to both cereal sole and maize-legume rotation systems.