The investigation of the mechanisms organic matter transformation in compost organic fertilizers is an urgent task of modern soil ecology and soil chemistry. The main components of such fertilizers are newly formed, weakly humified labile humic acids (HAs). The objective of the study is to determine the mechanism of converting the newly formed HAs into the forms with increased resistance to microbiological and biochemical influences. Obtained during the plant residues decomposition, HAs were studied in the incubation experiment (0, 30, 90 days). Calcium carbonate and biochar produced by rapid pyrolysis from birch and aspen wood, at 550 °C, were used as the composting mixture compounds. Decomposed plant residues—fresh aboveground mass of clover (Trifolium pratense L.), rye (Secale cereale L.), as well as dry oat straw (Avena sativa L.) were the material used for humification. To obtain Has, 0.1 M NaOH and 0.1 M Na ₄P ₂O ₇ were used. Then, HAs were separated from fulvic acids (FAs) using a 0.5 M H ₂SO ₄. The amount of labile HAs (HAs1) was estimated by their content in 0.1 M NaOH. The amount of stabilized HAs (HAs2) was calculated by the difference between the HAs content in 0.1 M Na ₄P ₂O ₇ and 0.1 M NaOH. Preparation of HAs for elemental composition and NMR analysis was performed according to the International Humic Substances Society’s recommendations. The possibility of converting newly formed HAs into stable forms (calcium humates), whose share in the HAs composition reaches 40–50%, has been shown. However, the mechanism of HAs transformation under the studied reagent’s influence was different. In the presence of calcium carbonate, it is caused by the physicochemical processes of newly formed HAs rearrangement. However, in the presence of biochar, this is due to the humification processes’ intensification and to the increase in the aromatization degree confirmed by the increase in the optical density, as well as by the increase in carbon and oxygen proportion, and by the decrease in hydrogen proportion in HAs molecules. The understanding of HAs formation and transformation mechanisms at the early humification stages can help to optimize the methods of obtaining organic fertilizers.