Soil Humus is of pivotal importance in the global ecosystem dynamics, since fluctuation in its amount and molecular composition affects not only the growth of both plants and soil microorganisms but also the main biogeochemical cycles. The development of technologies aimed at controlling humic substances (HS) in the agroecosystem processes is hindered by the limited knowledge of their chemical structure and dynamics. The recent recognition of the supramolecular nature of soil HS allowed us to devise a fractionation procedure, called Humeomics, that enables a detailed characterization of the structure of humic molecules in soil. Humeomics produces homogeneous fractions by progressively breaking esters and ether C–O bonds but not C-C bonds. The molecules in fractions are then identified by means of advanced spectroscopic and mass spectrometric techniques, thereby providing a large body of different chemical structures that may well be encompassed into the Humeome concept, inasmuch as other “omics” represent a multitude of the same species. Humeomics allowed to unravel the effects of different soil management practices on soil carbon dynamics and to explain the recalcitrance of humic matter in soil. Moreover, the application of Humeomics permitted to corroborate the novel concept of humification, that is unambiguously described as the progressive accumulation of hydrophobic molecular components, which are no longer accessible, due to their rapid thermodynamically driven partitioning from liquid to the solid soil phases. Conceiving Humeome as supramolecular associations of numerous relatively small compounds also helped to unravel its reactivity with respect to plant and microbial development, as well as to propose innovative technologies for the control of organic matter stabilization in soil. These are based not only on the stable incorporation of biolabile molecules into humic hydrophobic domains of soil and compost but also on the in situ photo-polymerization of humic molecules catalyzed by metal porphyrin biomimetic catalysts. In the latter technology, the resulting increase in molecular mass of humic molecules was found not only to increase soil aggregate stability but also to sequester in soil significant yearly amounts of organic carbon. Moreover, exogenous Humeomes isolated from geochemical materials such as lignites or from composted biomasses can exploit their supramolecular conformations to exert biosurfactant activity and be employed as effective agents in the removal of organic and inorganic pollutants from soil. It is expected that the research findings presented here on the versatile molecular activities of the Humeome will prompt novel studies on the man-driven control of the soil functions in order to increase carbon content in soil and contribute to positively affect both crop yields and soil microbial activity.