In vitro studies were undertaken to determine the effects of five fungicide and disinfectant treatments [propiconazole (Tilt 250EC), azoxystrobin (Amistar 250EC), didecyldimethyl ammonium chloride (Sporekill), alkali metal salts of alkylbenzene sulfonic acid and coconut diethanolamide (Farmcleanse), and potassium peroxymonosulfate (Virkon)] in preventing the germination of spores of Puccinia graminis f. sp. tritici, Kabatiella caulivora, Leptosphaeria maculans and Magnaporthe oryzae. Germination was inhibited by all fungicides and disinfectants, with maximum reductions at the manufacturer’s recommended concentration. Overall, azoxystrobin was the most effective, reducing germination of M. oryzae by 89%, L. maculans by 78% and P. graminis f. sp. tritici by 77%. Propiconazole was the most effective in reducing germination of K. caulivora by 72%. The extent of inhibition of germination was dependent on the pathogen; for example, alkali metal salts of alkylbenzene sulfonic acid and coconut diethanolamide, and potassium peroxymonosulfate were more effective on M. oryzae and P. graminis f. sp. tritici compared with L. maculans or K. caulivora. Studies undertaken to define the effectiveness of the fungicides/disinfectants reducing germination of the pathogens on five inert carrier materials (steel, fabric, wood, paper, and rubber) showed azoxystrobin and propiconazole to be the most effective, having 12–15% spore germination following decontamination treatment of carrier materials. The results demonstrate the potential for increased use of fungicides, particularly demethylation inhibitor and QoI fungicides, to decontaminate carrier materials to address the critical need to implement a practical commercial solution for dealing with threats posed by the long-term viability of these and other plant pathogens on inert materials associated with movement of humans, farming equipment, and commodities nationally and internationally.