The article’s main focus is the relationship between the re-established Bessarabian Orthodox Metropolitanate and the government of the post-Soviet Republic of Moldova. The article demonstrates that the Moldovan government refused recognition to the nascent church until 2002 primarily for two reasons: first and foremost, the Moscow Patriarchate opposed the idea of another Orthodox Christian church in Moldova outside of its jurisdiction; second, the government feared that the newly independent Republic of Moldova would fall under the influence of neighboring Romania, whose Orthodox Church offered patronage to the Bessarabian Metropolitanate. After a historical overview of the Orthodox Church in the Republic of Moldova, the article first presents and analyzes the history of the conflict between the Bessarabian Metropolitanate and the post-Soviet Moldovan government, and second, the European Court of Human Rights verdict ordering the government to recognize the Metropolitanate, before verdict’s implementation, and reactions to it. All these are done with an eye on intra-national relations among Moldova, Romania, and Russia, as well as those between the Romanian Orthodox Church and the Russian Orthodox Church in connection with this conflict.