Quarantine institutions are generally conceptualized as highly effective ways for states to extend their physical presence, power and sovereignty, especially in contested territories. A year after the second cholera pandemic (1829-49) swept through the province in 1846-47, it was announced that a quarantine infrastructure would be swiftly laid down in important border towns, as well as the major cities of Ottoman Iraq, which were gateways to merchants, pilgrims and disease from Iran and further East. With focus on the border town of Khanaqin, which was the busiest crossing between Iran and the Ottoman Empire, this paper asks what it meant for an Ottoman quarantine post to become operational institutionally in terms of human resources, finances, and space in the nineteenth century and whether these three elements were always in synchronicity. This institutional focus aims to capture how and in what ways the institution evolved in a single province within the context of the empire’s ambitious effort in the nineteenth century to centralize and modernize, termed as the project of the Tanzimat. Through a close look based on Ottoman archival documents, the paper shows that although Baghdad’s highly prioritized quarantine infrastructure was officially established in 1848, lack of financial resources as well as border ambiguities, meant that no purposeful infrastructure was laid down in the province until the 1870s. The paper adopts a comparative approach, making use of the growing number of studies on quarantine facilities around the empire. While Andrew Robarts suggests in his study of the quarantine complex in İzmir that “given the centralized, comprehensive and empire-wide nature of Ottoman quarantine administration in the middle part of the nineteenth century, it is reasonable to assume that the procedures in place in İzmir closely resembled those in place in other Ottoman quarantine administrations…” this paper argues that these resemblances had severe limitations, highly dependent on geography, state capacity and the broader geopolitical context.