Throughout his reign, Thomas waged a war with the Serbian Despotate over the lucrative mining town of Srebrenica and its surroundings, in addition to (or in conjunction with) multiple conflicts with his father-in-law.
Wishing to improve his image among Europe's Catholics, Thomas turned against the Bosnian Church, thus becoming the first ruler of Bosnia to engage in religious persecution.
Thomas' illegitimate older brother, Radivoj, unsuccessfully contested Tvrtko's rule with the help of the Ottoman Turks and the Kosača family, the leading magnates of the Kingdom of Bosnia.
However, the kingdom's most powerful magnate, Grand Duke Stjepan Vukčić Kosača, refused to accept Thomas as king, and announced his support for Radivoj.
[8] Because of this, Thomas hastened to send word of his accession to foreign rulers, including the German king Frederick IV, Ulrich's rival, and Ragusan and Venetian authorities, hoping to receive recognition.
[5] Ulrich was occupied with the feud waged against him by Frederick, as well as with the succession struggle in Hungary, where he had taken side with his cousin, queen dowager Elizabeth of Luxembourg and her infant son Ladislaus against the reigning monarch Vladislav I, leaving Thomas ample space of maneuver.
King Thomas tried to exact the promise of help from Venice in the event of a Hungarian offensive against him, even offering 25-year-long control over some of his towns and mines to the Republic in return.
The Turks were now ready to assist the Duke and broke into Bosnia, forcing the King to flee from Kozograd to Bobovac, and enabling Kosača to reverse all his losses.
[16] A rapprochement with Kosača via marriage with his daughter Catherine was probably already envisaged in 1445,[17] when Thomas improved relations with the Holy See in order to be cleared of the "stain of illegitimacy" as well as to receive an annulment of his union with Vojača.
[16] King Thomas was then finally converted from Bosnian Christianity to Roman Catholicism by Tommaso Tommasini, Bishop of Lesina;[18] however, Cardinal Juan Carvajal only performed the baptism in 1457.
[19] Thomas' intention to marry Kosača's daughter Catherine was made known in April,[16] their lands and borders reverting to status quo ante bellum.
The Bishop of Feltre and papal legate to Bosnia, another Tommaso Tommasini, fetched the crown from the Cathedral of Saint Domnius in Spalato in July, but it never reached Thomas.
At the request of Đurađ Branković, the Turks broke into both King Thomas' personal lands, and those of his father-in-law, in March 1448, plundering and burning towns.
[25] To finance this incessant warfare, as well as to sustain the royal court, King Thomas engaged in vigorous commerce and made business deals with Dalmatian traders.
[26][5] In 1451 when Kosača sought to improve his own economy through a war with the Republic of Ragusa,[27] Thomas refused to join either side, but still interceded with Pope Nicholas V to prevent his father-in-law's excommunication.
[28] In the summer, Thomas was even approached by Kosača's family, namely the King's brother-in-law Vladislav and mother-in-law Jelena, who were gravely offended when the Duke took his son's charming Sienese bride as his concubine.
[32] The coalition then suddenly fell apart when it became clear that Vladislav would not hand over parts of his patrimony that Thomas claimed as his due, namely Drijeva and Blagaj, which was the Kosača seat and the key to Zachlumia.
Another concern was the end of regency for the hitherto underage Hungarian king Ladislaus the Posthumous, which decreased the influence of Thomas' friend János Hunyadi, and led to the rise of Ulrich of Celje, who was supported by Kosača.
[35] In 1456, Thomas sent a letter to Pope Callixtus III asking him to find a bride for his son Stephen, hoping that the Holy See would provide him with a daughter-in-law of royal blood.
The heavy Ottoman defeat by Hungarians at the Battle of Belgrade in July 1456 did nothing to alleviate Thomas' situation, as Mehmed started exerting an even greater pressure on Bosnia.
Realizing that Hungary was drastically weakened, and that he had crossed the point of no return by refusing the Sultan's demands, Thomas decided to step forward to head the Christian coalition.
The death of the heirless Ulrich of Celje reopened the possibility of seizing Talovac lands, but his father-in-law moved more quickly, leading to a new brief cooling in their relations.
Thomas captured a total of eleven towns, keeping Srebrenica, Zvornik and Teočak for himself, and distributing the rest among the local nobility who swore fealty to him.
[42] A large Turkish raid in February 1458 forced Thomas to sign a truce, despite his earlier crusading vows, but Mehmed no longer insisted on the cession of the four towns; he intended to conquer Serbia instead.
That way Thomas procured not only a daughter-in-law of imperial blood, but also found a way to extend the Kotromanić rule to the Despotate of Serbia, now reduced to the Smederevo Fortress and its surroundings, as Lazar had left no sons.
During Thomas' long absence, Turks broke into Bosnia and besieged Bobovac and Vranduk, but his son Stephen and brother Radivoj escaped.
Thomas boasted about his son being made despot,[44] but the arrangement was cut short by the arrival of Mehmed at the head of a vast force before the walls of Smederevo.
[45][5] Unlike in other Balkan states of the time, the politics of Bosnia were not dominated by religion, and its rulers as well as the common people were entirely indifferent to the religious beliefs of others.
Thomas was forced to surrender northeastern Bosnia, namely Usora, Srebrenica, Zvornik and Teočak, in early 1460, allowing the Turks to cross the Sava to the Hungarian regions of Slavonia and Syrmia.
[52] Fickleness damaged his reputation abroad, while religious persecution and forced conversions caused disapproval at home;[54] he was cursed in the early years of the Ottoman rule for robbing the indigenous Bosnian Church of its property.