He took a leading part in the negotiation of 1890 for the Bohemian settlement, but the elections of 1891, in which the Young Czechs who were opposed to the feudal party gained a decisive victory, made his position a very difficult one.

Although he succeeded in bringing to a conclusion the negotiations with Hungary, the support he gave to the Czechs and Slovenians increased the opposition of the Germans to such a degree that parliamentary government became impossible, and at the end of 1899 he was dismissed.

He married for the second time in 1901 to his distant cousin, Countess Ernestine Gabriele von Thun und Hohenstein (1858–1948), widow of Count Eugen Wratislaw of Mitrovic (1855–1897).

They had one daughter, Countess Anna Maria Wilhelmine (1903–1943), who married her first cousin once removed, Baron Wolfgang von Thienen-Adlerflycht (1896–1942) and got Castle Neuhaus near Salzburg as a wedding present.

As he had only one daughter, upon his death in 1916 the Princely title was inherited by his brother, Prince Jaroslav von Thun und Hohenstein (1864–1929), uncle and legal guardian of the Hohenbergs, children of the murdered Archduke Franz Ferdinand of Austria and his morganatic wife, Sophie, Duchess of Hohenberg, who was sister of Jaroslav's wife Countess Maria Pia Chotek von Wognin (1863-1905).