About 107 million Russians are eligible to cast ballots and turnout was almost 60 percent an hour before polls closed in Moscow at 1700 GMT, according to figures displayed in the central electoral commission information centre.
Putin is facing seven challengers on the ballot but the outcome of the vote is pre-ordained, given his high popularity ratings. The government wants to ensure that this election is clean after ballot stuffing and fraud marred the last Russian presidential election in 2012.
Election commission representatives met Thursday with lawyers for opposition leader Alexei Navalny, whose supporters are seeking to observe the voting.
Some examples: ballot boxes being stuffed with extra ballots in multiple regions; an election official assaulting an observer; CCTV cameras obscured by flags or nets from watching ballot boxes; discrepancies in ballot numbers; last-minute voter registration changes likely created to boost turnout and a huge pro-Putin board inside one polling station.
His lawyer Ivan Zhdanov said the actual national turnout at 1700 GMT, when polls closed in Moscow, was 55 percent, according to data collected by monitors.
The Kremlin, however, is concerned about turnout.
But online groups set up to record voting violations reported hundreds of problems Sunday that cast a shadow over the official turnout figures.
Two election observers in Gorny Shchit, a rural district of Yekaterinburg reported witnessing an unusually high influx of people going to the polls between noon and 2pm.
The big push to get the vote out has been aided by a social media campaign.
But videos inside polling stations captured multiple breaches of electoral rules.
In Moscow, some people voting were offered free food to eat, while there was heavily discounted food available for sale elsewhere.
A wave of anti-government protests in the past year also suggests growing fatigue with corruption scandals seeping through the Kremlin and Putin's inner circle.
Russian Federation will remain a "difficult partner" after President Vladimir Putin's re-election but will be needed to help resolve worldwide tensions, German Foreign Minister Heiko Maas said today, questioning the vote's fairness.
Great-grandmother Valentina Ivanova, 76, explained to CNN in Moscow why she was voting. "What we care about is that this country have real, competitive elections". But the most important thing is peace. And I count on us all to continue this work together'. "My family are internationalists".
"I will not go to vote".
Putin's campaign spokesman Andrei Kondrashov alluded to the row with Britain over the poisoning of former Russian spy Sergei Skripal and his daughter.
Mr Putin, 65, has been in power, either as president or prime minister, since 2000. It's unclear so far if they'll back new measures to isolate Russian Federation, which denies any involvement.
In fact, he may be banking on confrontation with global players this election.
In the latest challenge, the Kremlin leader brandished new "invincible" nuclear weapons in his state-of-the-nation speech this month, amid confrontation with the US over allegations Russian Federation meddled to help Trump win.
Polls opened at 8 a.m. Sunday in Russia's Far East regions of Chukotka and Kamchatka. "I hope and believe that our friends will stand alongside us". Russian diplomatic buildings in Ukraine would be heavily guarded by Ukrainian police, it added.
Ultra-nationalist firebrand Vladimir Zhirinovsky took around 6 percent, former reality TV presenter Ksenia Sobchak was on 1.5 percent and other candidates were on less than a single percentage point each.