Crop production is an important parameter to consider when addressing the dual challenge of meeting global food demands and mitigating environmental damage. Most of the world’s undernourished people suffering from chronic hunger live in South Asia, which is the focus area of this study. Thirty-three different scientific studies contributed 104 complete sets of observations representing organic and non-organic farms. To analyse the difference in crop productivity between organic and non-organic farms, a meta-analysis was conducted with an estimation of effect size and by testing the statistical significance of relative organic yield over absolute non-organic yield. Based on the results of this study, average productivity of organic farms is approximately 5% lower than that of non-organic, but the difference is statistically insignificant with substantial variation among different crop types (cereals, legumes and non-legumes, fruit crops and other cash crops). Organic yield for legumes and non-legumes was 0.7% and 6% lower than that for non-organic, respectively. The productivity of organic farms compared to low- and high-input non-organic farms is found to be 13% and 8% lower, respectively. Similar yields between organic certified and default organic farms were found, as the yield gap is 3.5% for certified organic farms and 6% for default organic farms, respectively. The effect size estimate reflected that the magnitude of difference between the productivity of organic and non-organic farms is very small and statistically not significant among crop types, organic farm types and level of input in non-organic farms. So, future research should focus on promoting organic farming for sustainable organic production. It should also address issues of certification, marketing, soil fertility and plant protection, easing certification for smallholders, developing marketing networks, building soil fertility, conserving soil and water and biological pest management, all of which helps to generate more knowledge and information capitalising on the already available basis and resources for organic farming in South Asia.