In April 1986, workers temporarily closed the Manhattan-bound roadway on the upper level in order to repair the deck there.[44] The north-side subway tracks, underneath the Manhattan-bound roadway, were also closed during this time.[45] In December 1987, inspectors also shut one lane of the lower level due to a crack in the deck.[46] The New York City Department of Transportation published a list of 17 structurally deficient bridges in the city. Among them was the Manhattan Bridge, which needed $166 million in repairs to fix "cable anchors and torsion of steel members as subways cross".[47] Repairs on the northern side of the Manhattan Bridge were complete by the end of 1988,[43] and the subway tracks on the north side were reopened. Simultaneous with the reopening of the north side, the south-side tracks were closed.[48] In 1991, trucks were banned from the lower level because they were too heavy for the decaying bridge.[49]

"Major" repair work on the southern side began in 1992.[43] The Yonkers Construction Company was awarded a $97.8 million contract for the repair project in August 1992.[50] City Comptroller Elizabeth Holtzman originally denied the contract to the company because of concerns about corruption,[51] but she was overridden by Mayor David Dinkins, who wanted to complete repairs quickly.[50] At the same time, the NYCDOT increased the frequency of maintenance inspections for the bridge, after inspectors found holes in beams that had been deemed structurally sound during previous inspections.[52] The Brooklyn-bound roadway on the upper level was closed from 1993 to 1996 so that side of the bridge could be repaired.[53] The bridge repairs were repeatedly delayed as the renovation process uncovered more serious structural problems underlying the bridge. The original plans had been to complete the renovations by 1995 for $150 million, but by 1996, the renovation was slated to be complete in 2003 at a cost of $452 million.[41] By 2001, it was estimated that the total cost of the renovations had reached half a billion dollars, including $260 million for the south side and another $175 million for the north side. At the time, the NYCDOT had set a January 2004 deadline for the renovation.[54]

The original pedestrian walkway on the south side of the bridge was reopened after forty years in June 2001.[55] It was shared with bicycles until late summer 2004, when a dedicated bicycle path was opened on the north side of the bridge. The northern bridge bike path is notable for poor signage that leads to cyclist and pedestrian conflicts.[56] By the time work on the bridge was completed in 2004, the final cost of the renovation totaled $800 million.[23]

To celebrate the bridge's centennial anniversary, a series of events and exhibits were organized by the New York City Bridge Centennial Commission in October 2009. These included a ceremonial parade across the Manhattan Bridge on the morning of October 4 and a fireworks display in the evening.[57] In 2009, the bridge was designated as a National Historic Civil Engineering Landmark by the American Society of Civil Engineers.[