Milk clotting enzyme (MCE) of Moringa oleifera from prepared seed cake (PSC) dissolved in acetate buffer pH 5.0 recorded the highest activity compared to other samples, as well as 20–40% saturation of ammonium sulfate precipitated MCE with 28.20% yield and 1.01 purification fold. The proteolytic activity (PA) of crude MCE from Moringa oleifera PSC was higher than those of partial purified MCE with 180.81 and 155.47 as MCA/PA ratio, respectively. PSC moringa MCE exhibited their optimal activity at pH 5.0 and 60 °C; it could be capable to coagulate different milk types. Also, goat soft cheeses coagulated with moringa MCE exhibited significantly (p ≤ 0.05) higher levels of water soluble nitrogen content and total sensorial scores than control cheese. It could be concluded that partial purified MCE from Moringa oleifera PSC may prove to be a good candidate in goat cheese production without any appeared defects during their storage period.