The 73-year-old fiery nationalist will take an oath at parliament before heading to the presidential palace where Joko Widodo will hand over the reins after a decade in power.
It comes after a landslide first-round majority win in the February vote that critics said was aided by Widodo, more popularly known as Jokowi.
He is accused of activating state resources to help Prabowo and his running mate -- Widodo's eldest son 37-year-old Gibran Rakabuming Raka.
Security was heightened across the capital Jakarta ahead of the inauguration, with around 100,000 police and army personnel stationed including riot squads, sniper units and anti-drone teams.
The tight measures were in place with Prabowo expected to be paraded along the streets of Jakarta between the parliament and the palace.
Tens of thousands are expected to line the streets as he becomes Indonesia's eighth leader after the country achieved independence from Dutch colonial rule in 1945.
Several dozen state leaders were expected for the inauguration, with mostly regional politicians expected.
Australian Prime Minister Anthony Albanese had to cancel his visit as the British royals descended on Sydney.
- Disappearances -
NGOs and his former military bosses accuse Prabowo of ordering the abduction of democracy activists at the end of dictator Suharto's rule in the late 1990s.
According to the Commission for the Disappeared and Victims of Violence, or Kontras, 23 activists were kidnapped between 1997 and 1998.
Nine were found alive, one was found dead and 13 are still missing.
Prabowo was discharged from the military over the abductions but denied the allegations and was never charged.
Indonesian ally the United States once refused a visa over his rights record and he was also reportedly included on a visa blacklist in Australia before the 2014 election.
Both bans were reportedly lifted in the last decade.
Prabowo has also been accused of involvement in military crimes in East Timor, which Indonesia invaded and occupied in 1975 until 2002.
- Cuddly grandpa -
But a new image won over younger voters in this election, remodelling himself as a "cuddly" grandpa.
He shared images of his cats to his six million Instagram followers, while videos of him dancing went viral and painted him as the "everyman" candidate.
The decision to recruit Gibran as his running mate also proved popular but courted controversy after Widodo's brother-in-law passed a ruling to lower the age for candidates.
Yet their campaign surged after Gibran was allowed to run.
Gibran's popularity is tied to his father, who took Indonesia out of the Covid-19 pandemic relatively unscathed and back to five percent growth.
The incumbent president's successor has set an even higher target of eight percent growth within several years of his administration.
Prabowo has committed himself to Indonesia's non-aligned foreign policy but he has signalled that he will be bolder on the world stage.
He made China his first foreign visit after the election, before embarking on trips to a dozen other countries including Russia, Saudi Arabia and Australia, where he signed a key security deal.
Yet he railed against the European Union on the campaign trail for restrictions on deforestation-related products.
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