"This is the right moment to announce it," the Spanish coach said on Friday, ahead of what will be his final home game on Sunday. "Clarity is good for everyone."
The 43-year-old Alonso informed his players before Friday's training session that he was leaving, one year before his contract with the club expires in 2026.
Alonso, a former Real Madrid player, led Leverkusen to an unprecedented German league and cup double last season after taking over when they were in the Bundesliga's relegation zone in October 2022.
"I think that we can be happy, we can proud of what we have achieved during this time," Alonso said.
His Leverkusen team remain the only one to complete a Bundesliga season unbeaten, but they couldn't replicate that form this season and are eight points behind already-crowned Bundesliga champions Bayern Munich with two games left.
"I have tried to squeeze them as much as possible. They have given me so much, so maybe we are empty right now," Alonso said.
The Leverkusen job was Alonso's first in senior management job after a stellar playing career with Madrid, Liverpool, and Bayern.
He spent three years as a reserve-team coach at Real Sociedad, another former club. He started his coaching career at Real Madrid's youth setup.
Alonso declined to say where he will be going next.
"Now is not the day to talk about the future," said Alonso, who is reportedly the lead candidate to replace Carlo Ancelotti at Madrid.
Ancelotti is under contract until the end of next season, but is widely expected to be leaving after a campaign in which Madrid struggled despite adding Kylian Mbappe to its squad.
Ancelotti is scheduled to give a routine pre-game news conference on Saturday. He faces a huge match on Sunday when Madrid visit Barcelona, trailing their rivals by four points and needing a victory to keep alive their LaLiga title defence.
Brazil have been courting Ancelotti for over a year and it appears talks about the national team job are still ongoing with the veteran manager.
Ancelotti has repeatedly deflected questions regarding his future by saying he will announce his plans when the season ends.
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