Howson’s previous deal expired at the end of last term, and while discussions took place with the 37-year-old, he was not offered a new contract at the Riverside.
Details about Howson’s next move are expected to be revealed in the next few days, but he leaves with Boro’s blessings after achieving club-legend status in the last decade.
Signed under Garry Monk in the summer of 2017, Howson played under six different permanent Boro managers during his time on Teesside.
He made 341 senior appearances in his eight years as a Boro player, scoring ten goals, with his versatility seeing him appear in a variety of different roles.
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Initially signed as an attacking midfielder, Howson spent much of his time in a Boro shirt in a deep-lying central-midfield role, but also made regular appearances in the backline as either a right-back or centre-half.
His final Boro appearance came at Coventry City on the final weekend of last season, when his continued value and importance was emphasised by his appearance in Michael Carrick’s back four ahead of alternative central-defensive options.
A Boro statement said: “Jonny Howson has played his final game for MFC. The long-serving former captain was out of contract at the end of last season and has not been offered a new deal by the club.
“Signed by Garry Monk in the summer of 2017, Jonny also served under Tony Pulis, Jonathan Woodgate, Neil Warnock, Chris Wilder and Michael Carrick.
“His versatility and composure were a joy to behold and as club captain he led by example.
“MFC would like to thank Jonny for his wonderful service, commitment and dedication, and wish him all the very best for the future. Jonny will return to the Riverside in the coming months to say farewell to the supporters.”