According to The Times, the unnamed 21-year-old has been charged under a law against "insulting the feelings of religious believers".
The picture - which was taken last May but only recently brought to the attention of the police - was taken at the Church of St George the Victorious in Belgorod.
Critics of the law say that it is being misused by authorities to clampdown on those who oppose the Russian Orthodox Church; an ally of President Putin and the Kremlin.
Last year Youtuber Ruslan Sokolovsky, 22, was charged under the same law after he filmed himself playing Pokemon Go inside a church.
He has been held in police custody since October. No trial date has been set.