Christian higher education has been experiencing frequent transformational organizational change (e.g., downsizing, elimination of departments, technological innovations, addition of majors, etc.). These changes are significantly impacting faculty members. In other contexts, researchers have asserted that organizational change correlates with interpersonal conflict for employees and that such conflict is associated with counterproductive work behaviors (CWBs). If these associations are occurring for faculty members in Christian higher education, the result of CWBs as well as the consequences of conflict could result in lowered faculty engagement levels, turnover intentions, and other typical negative behaviors reflective of these variables in other contexts. Because faculty members in Christian higher education institutions are a vital link to student learning and faith integration within the curriculum, it is important for leaders to understand how change efforts might have unintended consequences that ultimately could undermine change efforts and impact the student experience. We utilized a multivariate analysis of theoretically identified variables related to CWBs, while examining faculty alignment with university values. A cross-sectional survey design assessed faculty (N = 267) perceptions of organizational change, interpersonal conflict, CWBs, and organizational identification at five Christian universities. The results indicated that organizational change was significantly correlated with interpersonal conflict and conflict was significantly correlated with CWBs. Organizational identification revealed an intervening effect on conflict and CWBs. A model applying open systems theory suggested that leaders in Christian higher education must consider the systemic effects of organizational change as they implement change initiatives.