The move comes with a buy option reported at around €15m and a 15 per cent sell-on clause for Frankfurt, who signed Theate permanently for approximately €13m from Stade Rennes last spring after an initial loan.
Should Bologna trigger the option, the Bundesliga club would turn a modest profit on a player who never quite established himself as first-choice at the Deutsche Bank Park.
Theate first played for Bologna during a loan spell in the 2021-22 season, before a permanent move to Rennes and, eventually, Eintracht Frankfurt. His departure leaves the Bundesliga side thin at centre-back, with Robin Koch and summer arrival Otávio now the only recognised options in that position, and Nnamdi Collins still working his way back from injury.
Frankfurt have responded by moving to sign Rennes defender Lilian Brassier as part of the same defensive reshuffle, viewing the swap as a like-for-like exchange in the position.
New Frankfurt boss Adi Hütter rarely used Theate during pre-season, a clear signal that his departure was coming even before Bologna's interest firmed up. For the player, the return to Italy represents a chance to rebuild momentum at a club where he already has a proven track record, rather than continuing to fight for a place in a Frankfurt defence being actively restructured around him.
Frankfurt sporting director Timmo Hardung thanked Theate for his contribution since arriving in Germany.
"We thank Arthur for the past two years and for his commitment in an Eintracht Frankfurt shirt," Hardung said. "He quickly developed into an important part of our team. We wish him all the best, personally and professionally, for his future in Bologna."
Theate leaves having made 75 competitive appearances across all competitions for Frankfurt, including 55 in the Bundesliga, and travels to Italy having also represented Belgium at this summer's World Cup, taking his tally to 36 caps for his country.