Returning organic materials to fields is an effective management practice for improving soil quality in agroecosystems. In the case of scarce organic material resources, choosing the optimal material type for improving the quality of a soil type is an urgent problem to be solved. The objective of this study was to evaluate the temporal variations in the spectroscopic characterization of humic acids (HAs) over a period of 90 days after applying biotechnologically extracted fulvic acid (BFA), well-decomposed sheep manure (M), corn stover pellets (Ps) and corn stover powder (Pr) at equal C amount to a chernozem under laboratory conditions, measured by Fourier transform infrared (FTIR) spectroscopy and ultraviolet-visible spectrophotometry (UV–Vis). The results indicated that the BFA and Pr with higher C contents (68.9 and 59.8 g kg−1, respectively) were more beneficial to the C mineralization of HAs. M, applied in the largest amount, together with the highest available N, P, and K contents (575.4, 160.1, 478.9 mg kg−1, respectively), and its more easily consumed carbohydrates as well as well-decomposed status, was more likely to promote the condensation of HAs. BFA carried more hydrophilic groups into the HAs, while Ps did not introduce high levels of adsorbed H2O molecules and aromatic C=C (or C=O) groups. Ps did not affect the molecular structure of HAs after incorporation into the chernozem. At the equal C input amount, M had the greatest benefit, whereas the beneficial effect of Ps was the least, in improving the chernozem quality.