Bekes was treasurer for John II Sigismund Zápolya, King of Hungary, and gained considerable power and favor with him. In his testament, Zápolya, who had no legal heir, designated Bekes as Voivode of Transylvania. However, the Hungarian nobles did not honor the will and elected Stephen Báthory as their voivode while Bekes was away on a diplomatic mission in the court of Maximilian II, Holy Roman Emperor. Supported by Maximilian, who opposed Báthory for the throne of the Polish–Lithuanian Commonwealth, Bekes gathered his army and organized a rebellion against Báthory, but was defeated. Bekes lost all of his possessions and was forced to seek asylum with Maximilian in Vienna. When Poland–Lithuania elected Henry of Valois as its monarch, Maximilian and Báthory ceased hostilities. Bekes unsuccessfully traveled to the Ottoman Empire seeking allies. His hopes were revived again when in 1574 Henry of Valois abdicated the Polish throne for that of France and the Maximilian–Báthory rivalry resumed. Bekes, supported by Székelys, started another rebellion, but his forces were defeated in the Battle of Kerelőszentpál in 1575. Supporters of Bekes were brutally suppressed and privileges for the Székelys were suspended.
Service to Báthory and death
In 1576, Báthory was elected and crowned a King of Poland and later became a Grand Duke of Lithuania, thus becoming the ruler of the Polish–Lithuanian Commonwealth. Maximilian died in 1576, and Bekes lost any hopes of reclaiming Transylvania. Bekes decided to reconcile with Báthory and became his loyal ally and close adviser despite differences in their religions. During the Danzig rebellion, Bekes commanded Hungarian troops, sent to assist Báthory in establishing his control over the Commonwealth, and gained special recognition for his defense of Elbląg. During the Livonian War againstIvan IV of Russia, Bekes joined the expedition to reconquer Polatsk. For his service Báthory assigned him Lanckorona and other lands. On his way to Hrodna Bekes caught cold, fell ill, and died later in Hrodna. His body was transported to Vilnius for burial, but none of the city's Christian cemeteries agreed to accept him because of his Unitarian faith. Therefore he was buried on a hill, which later became known as the Bekes Hill. His grave was marked by an octagonal tower, in height and in diameter. The hill and his grave were washed away by the Vilnia River in the mid-1800s. The territory is now within the Kalnai Park.