Her elder brother Archduke Ferdinand, succeeded as Holy Roman Emperor in 1619. On 7 February 1595 was received in Graz the formal petition of marriage between Maria Christina and Sigismund Báthory, ruling Prince of Transylvania, by the noblemen Stephen Bocskay. The marriage contract was negotiated almost a month, and finally the bride on 15 June accompanied by her mother, the Prince-Bishop George of Lavant and 6000 German horsemen.
In Kaschau Maria Christina fell ill with fever, which delayed the re-ride.
The formal marriage took place in Weissenburg on 6 August 1595, and soon after Maria Christina moved to Transylvania. The marriage was regarded as a major political gain, as Sigismund, formerly a vassal of the Ottoman Empire, now formed close ties with the Holy Roman Empire.
Emperor Rudolf II appointed Sigismund Prince of the Holy Roman Empire (Reichsfürst), and also secured the possession of Transylvania, if the couple remain without offspring. The agreement was signed on 16 January 1595 by the Hungarian parliament in Bratislava.
However, her rule was only nominal because Emperor Rudolf II sent representatives to rule.
When Sigismund abdicated for a second time in March 1599, Maria Christina finally left him and return to Austria in April.