The implementation of alternative cropping systems, including conservation agriculture (CA) and organic agriculture (ORG) in the La Cage experiment (France), and the organic waste products (OWP) application in the QualiAgro experiment (France) have led to an additional soil organic carbon (SOC) storage in ca. 20 years. The carbon sink effect of the soil will be more effective if the additional storage is realized in the form of persistent SOC, rather than labile SOC. The objective of this study was to evaluate the biogeochemical stability of additional SOC stored by alternative cropping systems and OWP applications including biowaste (BIOW), residual municipal solid waste (MSW) composts and farmyard manure (FYM). Biogeochemical stability was assessed using particle size and density fractionation and RockEval® thermal analyses on samples collected from both long-term experiments. The particle size and density fractionation isolated particulate organic matter (POM) and mineral associated organic matter (MAOM). The results showed that under OWP systems, 60-66% of the additional SOC was stored in MAOM and 34-40% in POM, whereas in alternative cropping systems, 77-84% of the additional SOC was stored in MAOM versus 16-23% in POM. In addition, soils with equivalent additional SOC stocks (MSW, FYM, CA) showed a higher additional carbon proportion in POM under MSW (40%) and FYM (33%) relative to CA (16%). This result suggests a higher chemical recalcitrance of POM in OWP systems, where POM comes from both plant residues and compost or manure particles, compared to alternative cropping systems, where POM only derives from plant residues. The PARTYSOC machine-learning model using Rock-Eval® thermal analysis parameters predict the active (30-40 years) and stable (>100 years) carbon pools as defined in the AMG model. The results revealed that most, if not all of the additional SOC belonged to the active SOC pool. These findings suggest that although additional SOC was predominantly MaOM and even associated with clays, it was probably not stored in a form with a mean residence time exceeding 30-40 years. However, the OWP promoted significant additional stable SOC storage (BIOW>MSW>FYM) compared to alternative cropping systems (CA>ORG). The OWP application and alternative cropping systems adoption resulted in substantial additional short-term SOC storage, but this storage will only be maintained at a high level if these "storage" practices are continued.