One of the primary challenges of our time is to enhance global food production and security. Most assessments in agricultural systems focus on plant yield. Yet, these analyses neglect temporal yield stability, or the variability and reliability of production across years. Here we perform a meta-analysis to assess temporal yield stability of three major cropping systems: organic agriculture and conservation agriculture (no-tillage) vs. conventional agriculture, comparing 193 studies based on 2896 comparisons. Organic agriculture has, per unit yield, a significantly lower temporal stability (−15%) compared to conventional agriculture. Thus, although organic farming promotes biodiversity and is generally more environmentally friendly, future efforts should focus on reducing its yield variability. Our analysis further indicates that the use of green manure and enhanced fertilisation can reduce the yield stability gap between organic and conventional agriculture. The temporal stability (−3%) of no-tillage does not differ significantly from those of conventional tillage indicating that a transition to no-tillage does not affect yield stability.