The persistence and efficacy of biocontrol agents (BCAs) in agricultural fields are crucial for sustainable crop production. In this study, using a novel qPCR probe protocol, we investigated the persistence of the introduced bacterial strain Pseudomonas sivasensis CF10PS3 in the wheat phyllosphere. The CF10PS3 strain, known for its biocontrol properties against wheat pathogens, was applied through foliar spray, and its persistence was monitored over seven weeks. Our qPCR assays, designed to specifically detect CF10PS3, distinguished it from naturally occurring P. sivasensis strains, providing precise insights into its dynamics in the field. The experimental results indicated that CF10PS3 was already present on the wheat leaves before application, suggesting its natural adaptation to the foliar environment. Following initial application, a significant increase in CF10PS3 was observed, though subsequent environmental factors such as rain and wind caused notable fluctuations in its population. Despite these variations, the introduced strain showed considerable persistence, with population levels significantly higher than those in untreated plots by the end of the study period. This research underscores the importance of understanding BCA dynamics in the field, highlighting the influence of environmental conditions on their efficacy. Specific qPCR probes proved effective in monitoring introduced strains, offering valuable insights for optimizing BCA application strategies. Our findings contribute to developing robust biocontrol methods, promoting sustainable agricultural practices and enhancing crop protection.