Abstract The Callide Oxy-fuel Project is the world's largest operating oxy-fuel plant. This work details an experimental test campaign at the Callide Oxy-fuel Project monitoring mercury and SO3 levels exiting the fabric filter during transitions between air and oxy firing conditions. The measurements were taken using two custom built probes; the first allowing combined collection of SO3 and mercury over short time intervals; the second allowing on-line measurements of Hgtotal and Hg0 with SOx removal. Total mercury emissions in oxy-firing measured a maximum of 6–7 μg/m3 of which 89% was in oxidised form (Hg2+). The use of low NOx burners had an overriding influence on the mercury measurements reducing the total mercury levels to 0.13 and 0.15 μg/m3 (air, oxy respectively) with no Hg2+ being measured. The SO3 concentrations were also lower than expected, estimated at ∼0.5–0.8 ppm (based on a practical estimate of 1% conversion of SO2). Overall mercury capture in either operating mode was estimated at 92–93% for the existing burners and 98–99% with the low NOx burners used (being 2 of the 4 burners operating). Total SOx captured from the flue gas was 16% in oxy-mode and 19% in air firing. These findings suggest that operational conditions have a primary impact on capture of Hg and SOx during transitions with a secondary impact of firing mode (i.e. air or oxy).