Background: Intraspecific variations in snake venom composition have been extensively documented, contributing to the diverse clinical effects observed in envenomed patients. Understanding these variations is essential for developing effective snakebite management strategies and targeted antivenom therapies. This study was prompted by the observations made by clinicians, who have noted significant variations in clinical outcomes among patients bitten by Naja mossambica in different regions of Africa, which links to the phenomenon of intra-species venom variability. We aimed to comprehensively investigate venoms from three distinct populations of N. mossambica from Eswatini, Limpopo, and KwaZulu-Natal regions in Africa in terms of their protein composition and reactivity with three commercial antivenoms (SAIMR polyvalent, EchiTAb+ICP, and Antivipmyn Africa). Methodology/Principal Findings: In contrast to previous reports, we discovered an unexpectedly high concentration of neurotoxic proteins in N. mossambica venoms (approximately 15%). The Eswatini population of Mozambique spitting cobra exhibited an increased abundance and diversity of neurotoxic proteins, including neurotoxic 3FTxs, kunitz-type inhibitors, vespryns, and mamba intestinal toxin 1. Immunochemical assessments of venom-antivenom reactivity unveiled differences, primarily related to low-abundance proteins. Notably, the reactivity of EchiTAb+ICP antivenom surpassed that of the widely used SAIMR polyvalent in serial dilution ELISA assays. Conclusions/Significance: Our findings reveal a substantial presence of neurotoxic proteins in N. mossambica venoms, challenging previous understandings of their composition. Additionally, the detection of numerous peptides aligning to uncharacterized proteins or proteins with unknown functions underscores a critical issue with existing venom protein databases, emphasizing the substantial gaps in our knowledge of snake venom protein components. This underscores the need for enhanced research in this domain. Significantly, our research highlights the superior reactivity of EchiTAb+ICP antivenom compared to SAIMR polyvalent, providing another compelling argument for its potential as an alternative to the commonly used SAIMR antivenom.