In 2003, he took up Estonian citizenship, keeping the Russian one.- Летом 2003–го вы получили эстонский паспорт. Российское гражданство при этом сохранилось?- Разумеется.</ref> In August 2008, Karpin was named as Director General of Spartak Moscow, replacing Sergei Shavlo. In April 2009, following a poor run of results, he replaced Michael Laudrup as caretaker manager of the club. On 18 April 2011, Karpin declared resignation from his position following one of the worse starts in club history. Eventually, he continued working as a manager up to the end of 2011–12 season.