There were calls for him to stay as manager of Algeria but he decided to quit and has now returned to the Black Sea club with its famously fanatical fans than he already headed from 2005 to 2006.
The 61-year-old Bosnian said he had turned down several highly lucrative offers from clubs in Europe and the United States to return to Trabzonspor.
"Money is important to live but it is not everything," he said after the signing ceremony in Trabzon. "I never thought of money in my life as a priority.
"It was an honour to receive offers from everywhere. But my only worry now is the success of Trabzonspor. The other offers were very good but I think words are more important than money."
Nonetheless, according to Turkish press reports, Halilhodzic's contract will be worth €3.3m over two years.
Halilhodzic said he would do his best to bring the team into the UEFA Champions League but admitted that the future was hard to predict.
Trabzonspor is the latest stop on the manager's varied career which has seen him coach teams from Côte d'Ivoire to Zagreb.
The Trabzon team finished fourth in Turkey's first division last season behind eternal Istanbul rivals but still winning a place in the UEFA Europa League.