Rising atmospheric carbon dioxide (CO2) concentration is increasingly affecting food production but how plant diseases will influence production and quality of food under rising CO2 is not well understood. With increased plant biomass at high CO2 the stubble-borne fungal pathogen Fusarium pseudograminearum causing crown rot (CR) of wheat may become more severe. We have studied inoculum production by Fusarium using fungal biomass per unit wheat stubble, stem browning from CR and the saprophytic fitness of Fusarium strains isolated from two wheat varieties grown in 2007 and 2008 at ambient and elevated CO2 in free-air CO2 enrichment (FACE) with or without irrigation and once in a controlled environment. Fungal biomass, determined using primers for fungal ribosomal 18s and the TRI5 gene, increased significantly at elevated CO2 in two of the three studies. Stem browning increased significantly at elevated CO2 in the 2007 FACE study. At elevated CO2 increased stem browning was not influenced by irrigation in a susceptible variety but in a resistant variety stem browning increased by 68% without irrigation. Wheat variety was significant in regression models explaining stem browning and Fusarium biomass but pathogen biomass at the two CO2 levels was not significantly linked to stem browning. Fusarium isolates from ambient and elevated CO2 did not differ significantly in their saprophytic fitness measured by the rate of colonization of wheat straw. We show that under elevated CO2 Fusarium inoculum in stubbles will be amplified from increased crop and pathogen biomass while unimpeded saprophytic fitness will retain its effectiveness. If resistant varieties cannot completely stop infection, Fusarium will rapidly colonize stubble to further increase inoculum once the crop is harvested. Research should move beyond documenting the influence of elevated CO2 to developing disease management strategies from improved knowledge of pathogen biology and host resistance under rising CO2.