Food security globally is highly dependent on crop production, which has been subjected to increasing pressures emanating from both an increasing demand for food and a deteriorating health of the agricultural ecosystem. Restoration of the ecological foundation for crop production has become a necessity in our pursuit for food security. As one of the most vulnerable natural resources, soils are becoming more and more degraded or polluted by agricultural and other anthropogenic activities. Soil organic matter (SOM), due to its close correlation with soil fertility and crop production, and high potential for carbon sequestration and nutrient cycling, has gained much attention in the last few years. In this policy paper, we argue that restoring SOM contents to optimal levels not only contributes significantly towards boosting crop production, but also improves the health of agro-ecosystems across the world. The study proposed a portfolio framework to bring all SOM-related issues together. Six categories of SOM Friendly Ecosystem Management (SFEM) were suggested to facilitate the SOM restoration process. Policy implications of the SFEM were also discussed for better understanding of the SFEM.