Council candidate Alejandra St. Guillen challenged the November election outcome after losing to fellow newcomer Julia Mejia by eight votes. The two had been vying for one of the council's four citywide, at-large seats.
Officials with the city Board of Election Commissioners were expected to begin the process of formally recounting about 66,000 ballots by hand Saturday.
The board says the count will likely last into Sunday and possibly into Monday.
Both candidates are community activists. They submitted petitions with at least 50 voter signatures from each of the city's 22 wards in order to trigger the recount.
The winner would become the city's first Latina councilor. She would also join Boston's most diverse council ever. When it takes office in January, the new council will boast both majorities of women and minorities for the first time.
Women will hold eight of the 13 council seats and there will be seven councilors of color.