Imposing military security measures as a consequence of violent conflict may lead to depressing economic effects for all parties involved. One implication is the limited ability to conduct trade, which in turn brings about welfare losses to the economic agents involved and may threat livelihoods and food security. This paper focuses on the consequences of the Israeli-Palestinian conflict, as a prominent example, on bilateral agricultural trade and price dynamics. For this purpose, we consider high-frequency wholesale price data and data on movement restrictions (complete closures) which were imposed by the Israeli Defense Forces in the West Bank between May 2007 and December 2008. In particular, we study the price dynamics of cucumbers and apples, two crops which play an important role for bilateral trade. The spatial and temporal price relationships are assessed using a cointegration framework. Specifically, we use a novel multivariate exogenous regime-switching vector error correction model and employ a recently developed extension of Johansen’s cointegration estimation method. We find the wholesale markets of cucumbers and apples in Hebron and Tel Aviv to be integrated. For both products, the price differentials between both markets quickly adjust to short run deviations from the long-run price equilibria. The regime-dependent model suggests that the movement restrictions effectively cut off both markets from each other temporarily.