Humic substances (HS) are heterogeneous organic compounds well known for stimulation of plant growth and development. The current study was designed to get insights about the physiological and metabolic processes induced by HS. Arabidopsis plants, grown hydroponically for 28 days on controlled conditions, were treated with HS at 1 mg C/L solution for 8 hours. iTRAQ (Isobaric Tag for Relative and Absolute Quantification) coupled LCMS (liquid chromatography–mass spectrometry) of HS vs control roots resulted in identification of 902 proteins species. 92 proteins showed significantly differential expression pattern (p-value ≤ 0.05) with a fold change of ≥1.3 for up regulated and ≤-1.3 for down-regulated proteins. Bioinformatic tools such as GeneCodis3, KEGG, STRING, IIS and Cytoscape were applied to comprehend the biological processes, molecular functions and pathways most targeted and the interaction networks amongst the identified proteins. Functional characterization and pathway analysis classified the identified proteins into different functional categories including response to inorganic substances, redox homeostasis, energy metabolism, cell trafficking and division. Many proteins related to protein synthesis, processing and translocation were also differentially expressed under HS application, for example, HSP70s, BiP2, PDIs and PABs. Three proteins, DPP6 N-terminal domain-like protein, patellin-2 and aspartyl protease family protein showed highest expression of 2.3 foldchange while germin-like protein subfamily 1 member 17 (GLP1-17) and cysteine proteinase RD19a revealed the lowest expression of -2.2 fold-change. The proteinprotein interaction (PPI) analysis generated a complex network consisting of seven significant modules. The main module contains 90 different proteins mainly associated with translation and biosynthetic pathways. Centrality analysis of the network identified topoisomerase II (Top II) as the most enriched hub/and bottleneck protein of the network. The enhancement of protein ubiquitination and stimulation of redox homeostasis and secondary metabolic pathways may explain the stimulation of signaling pathways and augmented growth of plants treated with humic substances. The xii DEPs identified in recent proteomic study may give some clues about the targets of HS and act as a podium for future study but more researches both at molecular and physiological levels should be done for find out of the HS metabolic target. The results of our in-silico promoter analysis of HS responsive promoter coding genes (HSRPGs) coincides with the proteomic study via linking the most enriched cis-acting regulatory (CREs) with stress, hormones, growth and developments. These results highlight the understanding of the underlying mechanisms involved in HS-plant interactions.