Molybdenum (Mo) is essential for many enzymes but is often sequestered within minerals, rendering it not readily bioavailable. Metallophores, metabolites secreted by microorganisms and plants, promote mineral dissolution to increase the metal bioavailability. However, interactions between metallophores and Mo-bearing minerals remain unclear. In this study, catecholate protochelin and hydroxamate desferrioxamine B (DFOB) were utilized to examine their effects on dissolution of the common Mo-bearing mineral, molybdenite (MoS2), under both oxic and anoxic conditions. Protochelin promoted molybdenite dissolution under oxic conditions, with the formation of MoO3 on the surface and Mo-siderophore complexes in solution. This was attributed to air-oxidation of both molybdenite and protochelin, as evidenced by lack of dissolution under anoxic conditions but enhanced dissolution by either preoxidized protochelin or preoxidized molybdenite. Liquid chromatography–mass spectroscopy, X-ray photoelectron spectroscopy, and time-of-flight secondary ion mass spectrometry analyses revealed degradation of protochelin and adsorptions of its byproducts on molybdenite surface to promote dissolution. Conversely, DFOB inhibited molybdenite dissolution under both oxic and anoxic conditions, likely attributed to surface adsorption of DFOB and its weak complexation with Mo(VI) at the circumneutral pH. This work highlights the need to consider the balance between promoting and inhibitory effects of different metallophores on Mo-mineral dissolution.