The decision has been made by Sunderland's board of directors and ownership.
Speakman joined Sunderland in December 2020 and oversaw the Black Cats' rise from League One back to the Premier League.
But Florent Ghisolfi arrived in the summer as the club's new director of football, which was the start of a transitional period behind the scenes. Ghisolfi has been leading Sunderland's strategy on and off the pitch since the summer so there won't be any day to day instability at the Academy of Light despite today's developments.
The transitional period has ensured Sunderland are now in an extremely strong position on and off the pitch. Speakman's exit is seen as the end of a defined chapter on Wearside.
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Chairman Kyril Louis-Dreyfus says Sunderland's "phase of redevelopment is now complete". He says the club's focus is now on "building from a position of strength with clarity of direction".
Ghisolfi, who joined from Roma, has led the football operation this season and was in charge of the summer recruitment that saw the Black Cats assemble a hugely impressive squad that is now competing for a place in Europe next season.
The Frenchman, who is understood to have now bought a house on Wearside and has told of his joy working for the club, has been putting the infrastructure in place behind the scenes since his summer arrival to ensure the Black Cats are in a position to build on their hugely impressive first season back in the Premier League.
Louis-Dreyfus said: “Kristjaan has made an important contribution to Sunderland AFC during a period of significant transition and growth, helping to rebuild the club and restore its place in the Premier League.
"Strong foundations have been established throughout our football operations over the past five years, and that phase of redevelopment is now complete.
"As we look to the future, our focus is on building from that position of strength with clarity of direction and sustained progress. We are grateful for Kristjaan’s commitment and professionalism and wish him every success for the future.”
In a statement, Sunderland said: "Kristjaan was a key figure during one of the most significant periods in the Club’s recent history, playing an important role in bringing Sunderland back to the Premier League.
Appointed in December 2020, he led a comprehensive rebuild of the Club’s football operations, reshaping its recruitment and performance infrastructure and restoring competitive momentum.
His time on Wearside included three victories at Wembley Stadium, including Sunderland’s first win at the national stadium since 1973 and two Play-Off Final wins."