Background: Moringa oleifera seed, which is widely utilized as an affordable source of domestic water treatment, is also reputable for its various pharmacological applications globally. Aim: This study evaluates the toxicity and pharmacological potentials of Moringa oleifera seed protein while establishing the chemical profile. Method: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography coupled with electrospray ionization mass spectrometry (LC-ESI-MS/MS) were used to analyze the protein/peptide content of the purified protein. The protein was also investigated for in vitro anti-cancer potential on Hela and MDA-MB-231 cell lines, cytotoxic on 3T3 cell line, and toxicity to brine shrimps. In addition, the antimicrobial action of the protein (polypeptide) was evaluated. Results and Discussion: The MALDI-MS revealed three protein moieties with values of 3.4, 4.6, and 6.9 kDa. On the other hand, LC-ESI-MS/MS analysis revealed dipeptides and tripeptides, which include serinylarginine, leucylproline, leucyl-methionyl-glycine, isoleucyl-glycyl-methinine, glycyl-arginyl-aspartic acid, isoleucyl-glutamyl-methionine, di-phenylalanine, asparaginyl-aspartyl-histidine, seryl-tyrosyl-tyrosine, phenylalanyl-asparaginyl-tyrosine, and propanolyl-trytophanyl-glycine. The seed protein exhibited extremely low toxicity on both 3T3 and MDA-MB-231 breast cancer cell lines, while the standards, doxorubicin, and cycloheximide had IC50 = 0.5 ± 0.07 and 0.8 ± 0.10 μg/mL, respectively. Further, the protein showed no antibacterial or antifungal activity against all tested organisms. The protein also exhibited no lethality against brine shrimp. The in-silico toxicity results indicated that the peptides are not immunotoxic, carcinogenic, or mutagenic as most belonged to the tox class V except serylarginine predicted for tox class IV (harmful if swallowed). Hence, the intake of the protein remnant in water could be within the tolerable limit. Conclusion: The results obtained suggested that the protein content of the Moringa oleifera seed is non-cytotoxic. The result further validates the safety potential of the defatted and debittered seed material used as potential food sources for both humans and animals.