Thomas was the son of Nikephoros I Komnenos Doukas and Anna Palaiologina Kantakouzene, a niece of Emperor Michael VIII Palaiologos.

Thomas' succession to his father's principality was endangered by the marriage of his sister Thamar Angelina Komnene to Philip I of Taranto, a son of King Charles II of Naples and Maria of Hungary in 1294.

Although Philip had been promised to inherit Epirus in his wife's right, when Nikephoros died between September 1296 and July 1298, Anna secured the succession of her son Thomas and assumed the regency.

In the meantime Charles II sent troops into Epirus, but they were repulsed and the Epirotes advanced into the Angevin lands in the western Balkans, recovering Butrinto and Naupaktos in 1304–1305.

A new Angevin invasion in 1307 ended with a compromise by which Philip of Taranto was ceded many of the fortresses that had been retaken by the Epirotes in the previous war.