Yury Dmitriyev was sentenced to three and a half years for abusing his fostered daughter.
He denies the accusations and his colleagues say he was framed in a plot to discredit his work.
The government of President Vladimir Putin has sought to downplay the extent of Stalin-era violence.
Dmitriyev, who has uncovered execution sites from the Great Terror in the 1930s, is expected to be freed later this year due to time already served.
His supporters received the verdict with relief and applause as he was given a much shorter prison term than the 15 years requested by the prosecution, BBC Russian's Oleg Boldyrev reports from Petrozavodsk.
Dmitriyev was accused by the prosecution of engaging in "child pornography". He was first detained in December 2016 after an anonymous tip-off.
When police searched his flat, they found images on his computer of his daughter, some of them naked.
A charge of non-violent sexual abuse of a minor was added the following year, as well as illegal possession of firearm parts.
Dmitriyev said the photos were taken to document the child's growth in case of problems with social services as she had been emaciated when the couple fostered her.