The purpose of the present study is to investigate, by means of thermogravimetric analysis (TG) and differential thermal analysis (DTA), diffuse reflectance infrared Fourier transform (DRIFT) and 2D nuclear magnetic resonance (NMR) spectroscopies, the structural features of the humic-like fraction (HLF) from olive pulp (OP), its effluents originated from the fermentation processes for hydrogen (EH2) and methane production (ECH4) and humic acid (HA) from soil amended with each of these materials. A considerable structural modification emerged between the HLF, in particular from the ECH4 effluent, which was characterised by a high content of polyphenolic and polypeptidic substances. The short-term amendment trial with OP and EH2 indicated that no chemical or structural changes in soil HA appeared. In contrast, the amendment with ECH4 substantially influenced the chemical and structural composition of soil HA. The structural interpretation performed by 2D NMR indicated the presence of aliphatic and aromatic protons while the sugar-like content and O-CH3 groups decreased with respect to the soil control HA. It emerges from this study that olive wastes contain stabilised humic-like material that may be recycled as an amendment in areas where olive trees are cultivated.