Last month Bulgaria's central bank put Botev's main sponsor, Corporate Commercial Bank, the Balkan country's fourth largest lender, under special supervision.
The move was followed by the departure of some of the club's leading foreign players and Bulgaria international Veselin Minev.
"I want to thank the management of Botev Plovdiv, the players, all who were close to the team, and of course the fans who supported us from the first moment," former Atletico Madrid and Valencia striker Penev told a news conference.
The 47-year-old replaced former Bulgaria coach Stanimir Stoilov at twice champions Botev on June 6, saying his work at the club would not affect the national team.
Botev, one of the most popular clubs in the country, finished fourth in the league last season and beat San Marino's Libertas 4-0 in the opening leg of their Europa League first qualifying round tie on Thursday.
(Reporting by Angel Krasimirov; editing by Josh Reich)
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