In 1788 he was once more promoted and as Gubernialrath he held a powerful  position in the administration of Transylvania. Müller was knighted by Leopold II to the lowest title of nobility, Edler, in the same year. From that point on he carried the name Franz-Joseph Müller Edler von Reichenstein. He was elected as a member of the Berlin Society of Friends of Natural Science.
In 1798 Müller became court counsellor and was appointed to the court in Vienna, where he was part of the imperial council. In 1818 Müller retired from his duties but held his position in the council until his death. He became Knight of the Order of Saint Stephen of Hungary in 1818 and became a noble by receiving the title of a Freiherr in 1820. Both honours were granted by the Emperor Franz I (II). Müller died in his 80s in 1825 or 1826 in Vienna.