Humic substances play empirically several essential functions in biogeochemical cycles such as storage of carbon, pollutants, nutrients and water, yet the underlying mechanisms remain poorly known because their precise molecular structure is largely unknown so far. Here, we extracted humic substances from biomass waste of bell pepper, fennel, artichoke, coffee ground, coffee husks, and nursery residues. We analyzed humic extracts by ultra-high resolution Orbitrap Fusion Lumos Tribrid 1 M mass spectrometry, using both positive photoionization and negative electrospray ionization modes, and by ¹³C cross polarization/magic angle spinning nuclear magnetic resonance spectroscopy. We identified 5000–7000 unique organic compounds in humic substances by integrating photoionization with electrospray ionization. The chemical distribution of all components was depicted by nuclear magnetic resonance. Humic substances from green composts are composed by a wide variety of hydrophilic and hydrophobic moieties, thus providing the required biosurfactant properties for effective soil washing capacities, with carboxyl-rich alicyclic molecules, fatty acids, and phenolic acids as major constituents. Overall, our findings provide a major insight in the molecular structure of humic substances, thus opening research on mechanisms ruling the origin, fate and behavior of humic substances.