Emperor Ferdinand I expected Elizabeth to promise in the proposed marriage treaty that Charles, as her widower, would succeed her if she died childless.

Unlike his brother, Emperor Maximilian II, Charles was a religious Catholic and promoted the Counter-Reformation, such as by inviting the Jesuits to his territory.

However, in 1572, he had to make significant concessions to the Inner Austrian Estates in the Religious Pacifications of Graz and in the 1578 Libellum of Bruck.

In 1580, Charles founded a stud for horses of Andalusian origin in Lipica, Slovenia and thus played a leading role in the creation of the Lipizzan breed.

Charles's mausoleum, in Seckau Abbey in which other members of the Habsburg family are also buried, is one of the most important edifices of the early Baroque in the south-eastern Alps.