The agroforestry systems with a high potential for C sequestration are those degraded by poor management strategies. Studies on changes in soil C status in these ecosystems mostly take into account labile C pools. Labile and stable soil organic matter (SOM) fractions are affected by soil management and land-use changes. Stable C pools are essential to understanding effects of land-use on soil C storage in the long term. The SOM stability is partly enhanced by the interaction of SOM with minerals and its inclusion into soil aggregates. Recalcitrant substances (e.g., lignin and chitin) also contribute to the passive SOM fraction. Macroaggregates mostly reflect the influence of plant roots and coarse intra-aggregate particulate SOM (POM), whereas microaggregates reflect the influence of fine interaggregate POM, clay concentration and humified SOM fraction. Often, POM is more sensitive to soil management changes than total SOM. Glomalin is a recalcitrant protein consisting of chitin produced by mycorrhizal fungi to protect hyphae. Glomalin has implications on C sequestration in agroforestry soils, but further research is needed before any prediction can be made. One challenge is reducing the CO2 emission from roots, and increasing the recalcitrant root C.