This study assessed different methods (tracheal and choanal cleft swabs from individual birds, and poultry dust as a population level measure) to evaluate the shedding kinetics of infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) genome in meat chicken flocks after spray vaccination at hatchery. Dust samples and tracheal and choanal cleft swabs were collected from four meat chicken flocks at 10, 14, 21 and 31 days post vaccination (dpv) and tested for IBV and NDV genome copies (GC) by reverse transcriptase (RT)-PCR. IBV and NDV GC were detected in all sample types throughout the study period. Detection rates for choanal cleft and tracheal swabs were comparable, with moderate and fair agreement between sample types for IBV (McNemar's = 0.27, kappa = 0.44) and NDV (McNemar's = 0.09; kappa = 0.31) GC respectively. There was no significant association for IBV GC in swabs and dust samples (R2 = 0.15, P = 0.13) but NDV detection rates and viral load in swabs were strongly associated with NDV GC in dust samples (R2 = 0.86 and R2 = 0.90, P<0.001). There was no difference in IBV and NDV GC in dust samples collected from different locations within a poultry house. In conclusion, dust samples collected from any location within poultry house show promise for monitoring IBV and NDV GC in meat chickens at a population level and choanal cleft swabs can be used for detection of IBV and NDV GC instead of tracheal swabs in individual birds.