In the first marriage, he married Agnes, a daughter of Count Enno III of East Frisia and in the second marriage Elizabeth Lucretia, a daughter of Duke Adam Wenceslaus of Cieszyn and herself a ruling Duchess of Cieszyn.

In 1606, the brothers signed a familial treaty stipulating that the first-born of the eldest surviving line would be head of the House of Liechtenstein.

Gundakar wrote a vindication, entitled "Motives that moved me to accept the Catholic faith".

In the following years he accompanied Archduke Matthias on military expeditions to Hungary and was present at the siege of Buda.

In 1606, he served several times as an ambassador and in 1608, he accompanied Matthias on his campaign in Bohemia against Rudolf II.

Then, at the beginning of the year 1619, he was sent as an ambassador to various princes, electors and prince-bishops to formally notify them of the death of Emperor Matthias.

In the same year, he undertook a second mission, to the spiritual electors, to prepare the election of Ferdinand II as the next emperor.

After the Imperial victory, Gundakar was tasked with punishing the supporters of the rebellion in Upper Austria.

However, he was displaced from that position by Hans Ulrich von Eggenberg, who was a supporter of Wallenstein and leader of the "Spanish" party at the court.

He also demanded that the state should promote the economy, in the sense of the early mercantilism, in order to increase tax revenue.

Like other Catholic noblemen loyal to the Emperor, he profited from the redistribution in 1619 of the dispossessed fiefs of the supporters of the Bohemian revolt.

He was enfeoffed by Ferdinand II with the Lordship of Uherský Ostroh, as a reward for services rendered.

He laid a claim on the County of Rietberg, which had been owned by his first wife, Agnes of East Frisia.

They had the following children: After the death of his first wife, he married in 1618 Elizabeth Lucretia, Duchess of Cieszyn (1 June 1599 – 19 May 1653).