Reepalu, 69, will bring his 19-year tenure to an end on July 1st. He addressed the anti-Semitism accusations, which have marred his latter years in charge, in a farewell editorial in newspaper Sydsvenskan, saying that his words had been misinterpreted.
Rabbi Shneur Kesselman, who has been on the receiving end of several anti-Semitic attacks, told The Local that he wouldn't miss Reepalu.
"This issue was not about somebody stepping down but about taking responsibility. I truly hope that whoever takes his place is more responsible," Kesselman said.
"Reeplau crossed the line on occasion with his comments and I just hope that his successor sees the reality of the situation," the US native added.
"Many Jewish people living in Malmö have lost their sense of security because of his comments. The problem goes much deeper."
At the beginning of 2011, Reepalu defended himself against anti-Semitism accusations.
"When people say that we have a right to take your land because we have some form of thousand-year promise from God that this is our land, then it creates conflicts," Reepalu said to the regional Sydsvenskan newspaper.
"Then they say that I am anti-Semitic when I put this across. I am flabbergasted that they are then able to tie all this together."
Frederik Sieradski, a spokesman for the Malmö Jewish community, told The Local that he didn't wish to make a political statement regarding Reepalu's imminent departure.
Sieradski did add, however, that he wasn't surprised the mayor was quitting as he approaches his 70th birthday.
"I just hope that the person who replaces him will cooperate with the Jewish community," Sieradski said.
"It is important that there be respect and understanding for all faiths."
Reepalu's work on revitalizing Malmö as a post-industrial city was praised by Jehoshua Kaufman. The organizer of the city's kippah walks said he didn't see a connection between the mayor's decision to quit and the anti-Semitism scandal.
"If you look at what he has done for the city, then he has been really good," said Kaufman.
"Reepalu transformed the city from a port town to a post-industrial place with a lot of enterprise. He changed the outlook of the city."
Kaufman suggested that Reepalu's issues with the Jewish community would inevitably play a part in defining his legacy.
"From the outside, he will probably be known as the mayor who was accused of anti-Semitism. It is a little unfair if that is all he is remembered for, but at the same time he only has himself to blame. I wish him well in his retirement."
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Reepalu's role in tackling Malmö's record deficit was hailed by his Social Democrat colleague Joakim Sandell. Upon taking the reins in 1994, Sweden's third largest city was 1.3 billion kronor ($206 million) in the red and had an unemployment rate of 22 percent.
"Malmö is an exceptionally different city now than before he took over. Now people want to move here, we have a university and landmarks like the Turning Torso," said the chairman of the Malmö Social Democrats.
Sandell also addressed the anti-Semitism furore, saying that Reepalu had been "deeply affected" by the accusations.
"Hopefully people will see the bigger picture and the role he has played in reorganizing the city."