Indaziflam, a broad-spectrum, pre-emergence herbicide was the focus of a field investigation conducted after the identification of sporadic injury symptoms on the pecan trees a few months after the application. The study was conducted in two pecan orchards located in southern New Mexico, USA, and southeastern Arizona, USA. The objectives of this study were to evaluate the occurrence and distribution of indaziflam in the soil profile of areas where pecan trees were injured (impacted) and areas where no injury symptoms were observed (unimpacted), and to determine the relationship between indaziflam concentrations and soil properties in those locations. Soil samples were collected, one year after applications, from six depth representing 0–7, 7–15, 15–30, 30–60, 60–90 and 90–120 cm depth to determine the concentration of indaziflam in impacted and unimpacted areas of the two orchards. Soil samples were analyzed to determine texture, bulk density, organic matter content, cation exchange capacity, pH, nitrate, chloride and calcium concentrations. The detection frequency of indaziflam was higher in Arizona than in New Mexico, likely due to the differences between the tillage practices and sand contents of the orchards. No significant correlations were observed between indaziflam and soil properties, however indaziflam was mostly detected in areas where pecan trees were unimpacted probably as result of greater organic matter content and soil porosity. More research is needed to understand the causes of injury to pecan trees by indaziflam application.