Camel whey protein (CWP) is rich in potent antioxidant and antimicrobial compounds, while the iron-based metal–organic framework (MOF)-235 offers high biocompatibility for drug delivery. This study synthesised and characterised CWP/MOF-235 nano-conjugates to enhance CWP stability, bioavailability, and therapeutic efficacy. GC–MS analysis confirmed the presence of hepatoprotective and antimicrobial fatty acids in CWP, including oleic acid, palmitic acid methyl ester, and cis-vaccenic acid. Antimicrobial assays revealed that CWP/MOF-235 exhibited greater activity against Candida albicans than CWP or MOF-235, achieving a maximum inhibition zone of 36.3 mm. Using earthworm (Aporrectodea caliginosa), cobalt chloride-induced chloragogen cell toxicity was effectively ameliorated by CWP/MOF-235, restoring normal intestinal histoarchitecture and reducing cellular necrosis as confirmed by light, scanning, and transmission electron microscopy. These findings demonstrate that CWP/MOF-235 nano-conjugates synergistically combine the bioactivity of camel whey proteins with the delivery potential of MOF-235, offering a promising eco-friendly strategy for managing heavy metal toxicity and microbial infections.