The presidential race is a re-match of the 2014 contest, with incumbent Joko Widodo taking on ex-general Prabowo Subianto.
Both have made political moves in line with the increased prominence of conservative Islam in the country.
Mr Widodo, looking to win another five-year term, is seen as the frontrunner.
Voters are now making their way to polling stations where they will vote by punching holes in ballots. They’ll also have their fingers dipped in ink to prevent double voting.
Both presidential candidates have cast their own votes – Mr Widodo in the capital Jakarta, and Mr Prabowo in Bogor, an hour’s drive south.
Polling is scheduled to close at 06:00 GMT and a series of “quick counts” are expected to give preliminary results within hours.
The election commission will announce the final result in May.
Analysts say the two main contenders have not presented wildly different policy platforms, apart from their views on Chinese investment.
“Therefore, the only contrast they can draw is by showing their religious credentials,” said Made Supriatma, a visiting fellow and Indonesia expert at the ISEAS-Yusof Ishak Institute in Singapore. “This election is a ‘race to the right’… a race to show who is more Islamic conservative.”
One Muslim voter told the BBC that “religion has been blown out of proportion in this election”
Muslim-majority Indonesia is made up of thousands of islands and has more than 260 million people. It is home to the world’s largest Muslim population.
Why is this election unique?
It will be the first time the country’s presidential, parliamentary and regional elections are all taking place on the same day. And with some 192 million people eligible to vote that makes it one of the biggest and most complex one-day polls in the world.
More than 245,000 candidates are running for around 20,000 national and local legislative seats.
Complicating things further is the geography of Indonesia – an archipelago of more than 17,000 islands.
Polling stations began opening in eastern Indonesia at 07:00 local time (22:00 GMT Tuesday). The country has three time zones, and western Indonesia, including the capital Jakarta, will vote from midnight GMT.
Voters – including those in remote and far-flung parts of the vast country – will have a window of only six hours to cast their ballots at one of the 810,000 polling stations that have been set up. However officials are likely to allow anyone already in line when stations close to cast their ballots.
Even before voting began the poll was hit with claims of vote-rigging. Indonesia launched an investigation last week after videos emerged appearing to show thousands of stray ballot papers at a warehouse in neighbouring Malaysia – many of them allegedly marked in favour of President Widodo. Close to a million overseas Indonesian voters are believed to live in Malaysia.