From 1987 to 1991 he was the first deputy Director of Ioffe Physico-Technical Institute. Since 2004 he has been chair of Rossiya Bank and its largest shareholder.
Since the early 1990s Kovalchuk has owned a dacha in Solovyovka in the Priozersky District of the Leningrad region, located on the eastern shore of the Komsomolskoye lake on the Karelian Isthmus near St. Petersburg. His neighbours there are Vladimir Putin, Vladimir Yakunin, Andrei Fursenko, Sergey Fursenko, Viktor Myachin, Vladimir Smirnov and Nikolay Shamalov. Together they instituted the co-operative society Ozero (the Lake) which united their properties on 10 November 1996. 
Kovalchuk was one of several individuals sanctioned by the U.S. Treasury Department on 20 March 2014 in response to the 2014 Crimean crisis. According to the U.S. Treasury, Kovalchuk is a close advisor to President Putin and has been referred to as one of his “cashiers.”