Food crop production declined by up to 66% in various Southern African countries as a result of El Niño induced drought during the 2015-2016 cropping seasons. This drought shock has led to emergence of food crisis throughout the region. This paper analyses the current drought impacts and how they are linked to historical droughts in order to draw lessons for building sustainable resilience mechanisms. The analysis uses both national and household level data. Evidence shows that up to early 1990s, drought shocks in Southern Africa were less frequent. During this period, the yields for major crops were generally low and stagnant. However, at the beginning of early 2000s the frequency of drought occurrence increased considerably. There was corresponding increase in yields of roots and tubers and vegetables in some countries, while yields for cereals and pulses remained more or less stagnant. Findings further show that in countries where there are considerable increases in yields of either roots and tubers or vegetables, there is a substantial decline in prevalence of undernourishment and food inadequacy. Overall, promoting nontraditional high value crops come out as key policy implications for resilience-improving interventions and food security improvements.