Rubin said they have reached an agreement in principle with Berdyev, who coached them from 2001 to 2013 and led them to two Russian Premier League titles.
Rubin general director Rustam Sayakhov said Berdyev's contract would be "long-term, well designed and structured.
The 64-year-old manager has also coached FC Rostov, helping the team finish second in the league last year and qualify for Champions League.
Rubin said Thursday it had parted ways with Spanish manager Javi Gracia after the club finished ninth in the league last season.
(Reporting by Moscow Newsroom; editing by Sudipto Ganguly)
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