Karimi, 31, a Sunni Muslim from Shiite Iran's Kurdish minority, ran into trouble with the powerful Revolutionary Guards over his documentary "Writing on the City".
The film details the history of scrawlings on Tehran's walls dating back to the Islamic revolution of 1979, through to the opposition Green Movement of the contested 2009 presidential election.
"The independent Iranian filmmaker Keywan Karimi on Wednesday began serving his one-year prison sentence in Evin prison," production company Les Films de l'Apres-Midi said in a statement, referring to a notorious Tehran jail.
"He will also receive 223 lashes."
Karimi spent 15 days in solitary confinement in 2013 when a trailer for the film was released on YouTube, accused of making "propaganda against the regime" and "insulting religious values".
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Since then several other charges were added including drinking alcohol, having extramarital affairs and making pornography, the filmmaker told AFP in a telephone interview in May, decrying the allegations as "ridiculous".
He was sentenced to six years in prison in 2015 but after an international outcry in which acclaimed Iranian directors including Jafar Panahi and Mohsen Makhmalbaf rallied to his support, five years of the term were suspended.
In May, during the Cannes film festival, more than 30 major European film organisations appealed to the Iranian government to grant him clemency.
But the filmmaker told AFP the sentence was "final" and that he had no intention of leaving Iran, although he hoped the penalty would be delayed as long as possible.
"I am not a political activist," Karimi told AFP. "I am not being sent to prison because I oppose the regime but because I am a filmmaker."
He had added: "The fact that my artistic activity is seen as an act of political opposition says a lot about the situation in Iran."
Karimi has made several short films including "Broken Border" (2012), a documentary about petrol smuggling, and premiered his first feature-length movie "Drum" at this year's Venice Film Festival.