The country has been bitterly divided in the run-up to Tuesday's re-run, the BBC's Emmanuel Igunza reports.
Widespread anti-government protests and violence have threatened to plunge Malawi into an even deeper crisis.
Whoever wins the election, will have to heal these deep divisions as well as tackle key electoral issues such as corruption, poverty and unemployment. Why is there a new vote?
A re-run of the May 2019 election was ordered by Malawi's Constitutional Court in February after judges found widespread irregularities with the original ballot.
That election saw President Mutharika narrowly re-elected by less than 159,000 votes with a 38.6% share of the vote. Mr Chakwera came second with 35.4%.
Mr Chakwera and the candidate who came third argued that the election had not been fair.
Their complaints included allegations that vote tallying forms had been added up incorrectly and tampered with using correction fluid - known in Malawi by its brand name Tipp-Ex. Getty Images
First election on 21 May 2019
Mutharika sworn in on 27 May 2019
Thousands protest on 20 June 2019, complaining of fraud
Constitutional court overturns result on 3 February 2020 and orders re-run
Court rejects Mutharika's appeal on 8 May 2020 Source: BBC
Uncertainty around the result sparked months of tension and protests, which spilled over into clashes between opposition supporters and police across the country.
February's decision to annul the election led some to celebrate, but Mr Mutharika described it as a "serious subversion of justice" which marked the death of the country's democracy.
Last month, Malawi's former electoral commission chair Jane Ansah resigned following months of pressure by protesters who criticised her handling of the poll.
The new vote comes at a time of growing tension between the government and the country's courts.
There have also been concerns over the logistics and safety of carrying out an election in the midst of the worldwide coronavirus pandemic. Who is in the race?
The president and his Democratic Progressive Party (DPP) are in an alliance with another party, the United Democratic Front (UDF). Reuters Candidate for the Democratic Progressive Party
Born 18 July 1940
Law professor taught in Ethiopia, Tanzania and USA
Brother Bingu was Mutharika was president, died in office in 2012
Arrested in 2013 accused of plotting coup but never charged
Won 2014 election after beating incumbent Joyce Banda Source: BBC Monitoring
"If you give me another five-year term, this country will develop to the level of South Africa or Singapore, London, America or Canada," President Mutharika told a campaign rally in the capital, Lilongwe, last week.
Mr Mutharika, a former law professor who taught in the US before becoming a cabinet minister, was first elected to Malawi's top office in 2014. Two years earlier his brother, Bingu wa Mutharika, died while serving as president.
He faces competition from Mr Chakwera, a former cleric who heads up the opposition Malawi Congress Party (MCP).
Born in Lilongwe to a subsistence farmer, the philosophy and theology graduate has pledged to raise the national minimum wage among other changes. AFP Candidate for the Tonse Alliance
Born 5 April 1955
Studied theology in Malawi, South Africa and USA
Pastor and lecturer worked at the Assemblies of God School of Theology
Authored several books on religion including Reach the Nations
Ran for president in 2014 and came third Source: BBC Monitoring
Mr Chakwera is leading a nine-party opposition coalition, the Tonse Alliance, and has the backing of former President Joyce Banda as well as the country's vice-president, Saulos Chilima, as his running mate.
Mr Chilima - who finished third in the 2019 vote - was once an ally of President Mutharika, but has since fallen out with him.
The vice-president has tried to reassure the public that the result will not see a repeat of the controversies of last time.
"Do not be discouraged; come out in large numbers to cast your vote. Your vote will be protected and no room for rigging," he said on a campaign visit last week. Related Topics