Early identification of social, emotional, and behavioral difficulties (SEBDs) in children is essential to provide support and reduce the risk of negative outcomes. Schools are considered ideal settings to identify SEBDs, and in many countries special educational needs coordinators (SENCOs) play a pivotal role in this respect. Although SENCOs may contribute to improving school-based identification of SEBDs by adopting a more systematic approach, they have a multitude of tasks and considerable professional discretion. As a result, there are differences between SENCOs in the quality of their identification practices in terms of the frequency of observations, the maintenance of a four-eyes principle, and the utilization of specialist knowledge, affecting whether and when SEBDs are identified. The aim of this study was to examine what factors can explain differences in these practices for early identification of SEBDs. Using a narrative qualitative approach, we interviewed 34 primary school professionals, studied school policy documents and observed team meetings. Thematic analysis revealed that an interplay of the factors: (1) (conformity to) school regulations, (2) team continuity, and (3) personal characteristics, explains why SENCOs decide differently on who conducts observations, and when. Generally, SENCOs are more likely to conform to frequent observations by at least two observers utilizing specialist knowledge, when schools have regulations that clearly define by whom and when observations should take place, with competent, committed, proactive school staff conforming to those regulations, within a stable team. Although each factor is important but not essential to ensure these practices, personal characteristics of the SENCO can compensate for a lack of clear school regulations or team discontinuity. Implications for school policy and practice are discussed.