About 16% of Dutch children are reported to have social, emotional, and behavioral difficulties (SEBDs). SEBDs generate distress and pose risks for various negative outcomes; thus, their timely identification is deemed important to respond appropriately to children’s needs and avoid such negative outcomes. Primary schools are considered convenient places to implement early SEBD identification, but the ways in which schools achieve this in practice may be inadequate, although the issue remains under-researched. Although there are several systematic school-based early identification methods (e.g., universal or selective screening), primary schools predominantly rely on school staff to recognize children at risk for, or experiencing, SEBDs. As differences in identification practices could impact whether and when (signs of) SEBDs are identified, this study aimed to increase our understanding of differences in identification practices used by school staff and their potential implications for early identification effectiveness. Thirty-four educational and clinical professionals working at nine primary schools participated in in-depth semi-structured interviews. We used MAXQDA to thematically code and analyze the data. Our analysis of these interviews illustrated that schools’ identification practices differed on three elements: the frequency of observations, maintaining a four-eyes principle, and the utilization of specialist knowledge. We argue that differences in these elements have potential consequences for the timeliness and quality of SEBD identification.