Jokowi, as the incumbent is known, has not explicitly endorsed any of the three candidates vying to replace him as leader of the world's third-largest democracy. But he has made highly publicised appearances with Prabowo, and his eldest son is running on the same ticket for vice president.
Two opinion surveys last week projected Prabowo could secure more than 50% of the votes on Wednesday, allowing him to win in a single round. Rivals Anies Baswedan and Ganjar Pranowo were seen at least 27 and 31 points behind him respectively.
Some voters have taken issue with Jokowi's perceived lack of neutrality, saying it undermines Indonesia's democracy by giving one candidate an unfair advantage.
Students gathered in Yogyakarta on Java island, banging bamboo instruments and holding posters painted with "bring Jokowi and his cronies to justice".
"Jokowi was once called a new hope, we call him a new disaster," one demonstrator said.
The protest organiser, Aksi Gejayan Memanggil, said on Instagram, "the ethical and moral breaches by Jokowi show that he is against a critical public voice."
Another protest was planned in the capital Jakarta by several rights groups.
The presidential office has denied political meddling by Jokowi.
The planned protests come after a documentary produced by an Indonesian investigative journalist, Dandhy Laksono, alleged that state officials including police and regional heads, and government welfare resources, have been used to favour Prabowo.
The film, "Dirty Vote", released at the weekend, had garnered nearly 5 million views on YouTube by Monday evening.
Reuters could not independently verify the allegations made in the documentary.
Prabowo's campaign team has dismissed the accusations and described "most of the contents in the film as defamatory".
The government has said social welfare is not being used to benefit any candidate.
The student protests also come as Indonesia enters a cooling-off period until voting day on Wednesday. Authorities were seen removing election billboards and posters, and candidates are barred from campaigning during this period.
Indonesia's police will deploy around 25,000 anti-riot personnel to ensure security during the election.
