"This is the only way to halt the crisis surrounding the editorial team and minimise the reputational damage," the independent news website quoted its chief editor Ivan Kolpakov and co-founder as saying.
His resignation is highly unusual in Russia where the Western #MeToo movement has largely failed to take off and rampant sexual harassment is often seen as a joke rather than a problem.
Kolpakov said at the time he did not remember anything but publicly apologised for his "ugly" behaviour. He was however reinstated by the board of directors and the employee whose wife was harassed later quit.
There is no legislation that protects women against sexual harassment at work or home in Russia.
A parliamentary ethics panel later cleared his name and Slutsky claimed the scandal had actually "boosted my gravitas".
Meduza, which is based in EU member Latvia to circumvent censorship, frequently writes about gender-based violence and harassment.
The site's management however admitted it had no guidelines on how to deal with such offences and found itself in unchartered waters.
When Kolpakov resigned, he said he was only doing so to protect the online publication from the growing controversy.
"I categorically refuse to accept the charges of harassment," he wrote on Facebook.
"I am leaving because it hurts me to see you destroy what I've built," he said of his critics.
Others said the incident had been blown out of proportion.
Mitya Aleshkovsky, a prominent Russian journalist and social activist, said that Kolpakov's actions could be described as "a bad joke, hooliganism (or) unworthy behaviour." "You can call it what you like, but this is not harassment," he said on Facebook.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)