Intergroup relations in protracted conflicts are typically analyzed in light of the conflict’s intrinsic dynamics. Yet, in recent years, global changes have increased the occurrence and intensity of shared exogenous threats such as extreme weather, natural disasters, and global pandemics. Do such shared external threats influence the willingness of groups in conflict to collaborate and assist one another? The literature produces inconsistent expectations. While some studies find that environmental and health crises can promote superordinate identities and cooperation, others argue that they deepen intergroup competition and ethnocentrism, and still others claim that they lack discernable impact on existing tensions. Our study explores this unresolved question in the context of the Israeli-Palestinian conflict amid the COVID-19 pandemic. Exploiting the spike in COVID-19 cases in both societies, we conducted a two-wave survey and a conjoint experiment among Israeli Jews to examine the extent and conditions under which they would support policies that fight the virus’s spread in the adjacent Palestinian territories. We find that the pandemic’s threat did not change the conflict’s core dynamic. Support for medical assistance, preference for improving the Palestinians’ situation, and willingness to collaborate with their leadership reflect partisan ideology and sense of national threat by the Palestinians rather than the anxiety and threat caused by the pandemic. These findings provide a sobering perspective on the expectation that shared exogenous threats could change existing intergroup dynamics in active conflicts.