After temporarily acquiring Portuguese ‘possessions’ in Flores and islands immediately to the east in 1851, the Netherlands East Indies took full possession in 1859. An important condition guaranteed religious freedom to Catholics in the transferred territories. Dutch authorities took this concession seriously and requested that Dutch Catholic missionaries be sent to Larantuka, Flores. Eventually the Jesuits assumed responsibility. The Dutch Catholic priests objected to many aspects of local ceremonial practice and in particular to the local temples. Their efforts to abolish these temples and practices involved them in local disputes and eventually in a war. This article examines the complexities of the resulting events and in particular the tensions among the priests, colonial authorities and local leadership.