Upon his return, he made enemies with the powerful Embriaco family, which governed Byblos through Guy II. Tripoli was very weak at this time and was divided among various factions: the Roman faction led by Paul of Segni, bishop of Tripoli, and the Armenian faction led by Sibylla and Bartholomew. Paul made friends with William of Beaujeu, the new grand master of the Knights Templar, and then with the normally anti-Templar Embriacos. This precipitated the first of a series of wars between Bohemond and the Templars. First, he burned their building in Tripoli. Then, the Templars responded by razing the comital castle of Botron and attacking Nephin. Bohemond marched on Byblos but was defeated and forced to sign a truce.
In 1278, Guy of Byblos and the Templars assaulted Tripoli, but were met outside the walls by Bohemond. Bohemond was defeated, but the Templar fleet of twelve galleys was scattered by a storm and Bohemond's fleet of fifteen attacked and damaged Templar Sidon. This time a truce was mediated by Nicolas Lorgne, grand master of the Hospital. The last conflict began in January 1282, when the Embriacos tried to take Tripoli by surprise. They found the Templar master away and so took refuge with the Hospitallers, who handed them over to Bohemond on condition that he would spare their lives. He buried them up to their necks in sand at Nephin and starved them to death. This last act further alienated the Genoese and John of Montfort, but Bohemund beat the latter in taking control of Byblos.
In 1287, Latakia was taken by Qalawun, who claimed that as part of Antioch it did not fall under the conditions of their treaty. Bohemond died soon after, leaving no children by his wife Margaret of Beaumont. Tripoli was plunged into a succession crisis until his sister Lucia arrived from Europe to take control of the county.
Sources
Setton, Kenneth M. (general editor) A History of the Crusades: Volume II — The Later Crusades, 1189 – 1311. Robert Lee Wolff and Harry W. Hazard, editors. University of Wisconsin Press: Milwaukee, 1969.