Problems loomed large as Abbas started off his first day as president of the Palestinian Authority (PA), calling for a mutual ceasefire with Israel and for an end to violence on both sides of the conflict.
The first sign of trouble came when two senior members of the electoral commission, Ammar Dwaik and Baha al-Bakri, resigned in protest on Saturday, saying they wanted to warn the public that voting irregularities and pressures could be repeated in legislative elections in July.
They said gun shots were fired at the electoral panel's headquarters during a Central Election Commission meeting to consider the requested changes. Electoral officials said they recognised at least one member of Palestinian intelligence firing at the building.
The officials said they did not believe the change in voting procedures significantly altered the outcome of the vote.
Abbas, the Fatah candidate, won 62.3% of the vote. "These pressures and threats lessoned the degree of the integrity of the election, even though overall it was free and fair," said Dwaik, the deputy chairman of the commission.
During the presidential election, polls were to have stayed open for 12 hours, until 7pm. However, several hours after polls opened, turnout was relatively light, a cause of concern for Abbas, who was the frontrunner but needed a decisive victory to win a mandate for peace talks with Israel.
"We were visited by senior officials from Abu Mazin's campaign, and we were pressured to change procedures on election day," al-Bakri said. Abbas is widely known as Abu Mazin.
In the end, the commission decided to extend voting by two hours and to allow voters to cast their ballots in any location, not only in their hometowns.
"We were visited by senior officials from Abu Mazin's campaign, and we were pressured to change procedures on election day"
Senior member of the Central Election Commission
The change enabled thousands of members of the security forces, most of them Abbas supporters, to cast ballots near their posts rather than travelling to their hometowns, some of them a distance away.
Dwaik and al-Bakri said on Saturday that those decisions were made under pressure from Abbas' campaign, Fatah and the intelligence service.
"I was personally threatened and pressured," Dwaik said. "I am therefore announcing my resignation publicly, so that everyone knows that in the upcoming legislative election, this could happen again."
Al-Bakri said voting hours are extended only in cases where there are long lines at the polling stations. "This was not the case on election day," he said.
"These procedures had two goals, first to increase the turn-out, and second, to increase the percentage of Fatah voters," al-Bakri said.