A method and system for in-process cleaning of an ion source (12) is provided. The ion source (12) comprises (i) a plasma chamber (22) formed by chamber walls (112, 114, 116) that bound an ionization zone (120); (ii) a source of ionizable dopant gas (66) and a first mechanism (68) for introducing said ionizable dopant gas into said plasma chamber; (iii) a source of cleaning gas (182) and a second mechanism (184) for introducing said cleaning gas into said plasma chamber; and (iv) an exciter (130) at least partially disposed within said chamber for imparting energy to said ionizable dopant gas and said cleaning gas to create a plasma within said plasma chamber. The plasma comprises disassociated and ionized constituents of said dopant gas and disassociated and ionized constituents of said cleaning gas. The disassociated and ionized constituents of said cleaning gas react with said disassociated and ionized constituents of said dopant gas to prevent formation of deposits of elements contained within said ionizable dopant gas on surfaces of said chamber walls. The cleaning gas may be, for example, nitrogen trifluoride (NF 3 ), and the ionizable dopant gas may be, for example, either phosphine (PH 3 ) or arsine (AsH 3 ). Mass flow controllers control the ratio of cleaning gas to ionizable dopant gas introduced into said plasma chamber, which is greater than 0:1 and preferably at least 3:1.