The project was intended to remove or reduce the need for subway transfers for a large number of riders with jobs on the east side of Manhattan.

Afterward, work began on other facilities related to the line, such as new platforms at Grand Central, ventilation and ancillary buildings, communication and utility systems, and supporting rail infrastructure in Queens.

[9] According to renderings of the transportation center, the mezzanine would be placed above four island platforms and eight tracks, which would be split evenly across two levels,[8]: 48–49  similar to the present terminal under Grand Central.

"[22] Richard Ravitch, the MTA chairman, said that to stop the work was impossible or so costly as to make it impractical subsequent to the construction of the subway portion.

[36] At first, MTA officials held fast to their plans,[37] but after continued opposition, they reduced the size of the building and moved the structure's cooling towers.

[28]: 3 [10] An upper-level concourse, accessed by a series of stairs, elevators, and escalators,[47] would replace ten tracks on the west side of Metro-North's Madison Yard.

The instruments include inclinometers, extensometers, seismographs, observation wells, dynamic strain gauges, tilt meters and automated motorized total stations with prismatic targets.

[44]: 16, 18  In 2010, the New York City Business Integrity Commission found that a subcontractor for the East Side Access project was involved with an organized crime family.

[54] In July 2011, after the tunnel boring machines finished drilling through the Grand Central station box, they were left in place under 38th Street and Park Avenue, as it was more economical than disassembling them in Queens and selling them for scrap, which could have added $9 million to the project's final cost.

[58] The park, containing abundant greenery along a granite backdrop with tables and chairs,[59] was meant to reduce noise pollution from the ventilation facility, which also served as an emergency exit.

It created an area that served as the launch chamber for soft-bore Queens tunnels that would connect the 63rd Street line to the main LIRR branches, and an interlocking and emergency exit and venting facility.

[85][86] In July 2018, workers started realigning tracks to make way for the construction of the Queens tunnel portal, which was the final major contract not underway at the time.

[93]: 9–10  On October 31, 2021, Governor Kathy Hochul rode the first passenger test train through the East Side Access tunnels to Grand Central Terminal.

[102][103] The Grand Central Madison station remained unopened two weeks later; MTA chairman Janno Lieber attributed the delays to a single ventilation fan that could not exhaust enough air.

[140] In the June 2022 MTA board meeting, chairman Janno Lieber described increased reverse-peak service as having a "potential boom to Long Island's economy".

[141][142] Riders have also criticized the elimination of timed connections at Jamaica, which will no longer be built into the schedule; the MTA claims that this change will reduce delays and allow more trains to run.

[141] On September 28, 2022, following backlash from customers, the MTA announced the restoration of three express trains serving Penn Station on the Port Washington Branch, which were initially cut from the draft timetables.

[162] Passengers who frequently traveled to Grand Central Madison said that the new terminal did not have the right amount of service, had a confusing station layout, and did not have enough restaurants and eateries.

[162] The opening of East Side Access saw the LIRR run 41 percent more trains per day, including substantial increases in reverse-peak service.

[171][83][84]: 36  As of July 2020[update], the MTA had a "target revenue service" date of May 2022 (whereupon construction would be essentially complete), while the line was planned to open to the public in December 2022.

[181][169] In 2015, the USDOT's Deputy Principal Assistant Inspector General for Auditing and Evaluation, Joseph W. Come, testified before the United States House Committee on Oversight and Government Reform's Subcommittee on Transportation and Public Assets.

Cost increases also occurred due to changing the design while construction was underway; ordering components that were the wrong size; failing to cooperate with other transit agencies in Sunnyside Yard; and making infeasible construction-timeline estimates.

[83] In a bid to lower costs and reduce delays, in September 2018, the LIRR hired Arthur R. Troup, who previously held senior positions with Atlanta's and Washington, D.C.'s rapid transit systems, to lead the East Side Access project.

[185][186] In October 2014, a contractor who was digging wells on the Queens side accidentally punctured the subway tunnel underneath, grazing an F train with passengers inside.

When the MTA planned the facility in 2002, it had anticipated that East Side Access would open in 2011 and that the Arch Street Shop could be used to maintain the LIRR fleet.

[196]: 20–21  In its 2015–2019 capital program, the MTA had budgeted $76.5 million for the construction of such a station[198] with a proposed start date in January 2021,[199] but then delayed any work until after the completion of East Side Access.

[11] Related to the MTA's East Side Access project is its long-planned widening of the two-track LIRR Main Line by adding a third track.

[212][213] Five "readiness projects" are also under construction across the LIRR system to handle the expanded peak-hour service planned when East Side Access opens.

[214][215][216] The largest of these projects is at Jamaica station, where the MTA is re-configuring track layouts, installing high-speed switches, and adding a new Platform F for the Atlantic Branch.

This new capacity, as well as track connections resulting from the East Side Access project, allows Metro-North Railroad trains on the New Haven Line to run to Penn Station via Amtrak's Hell Gate Bridge.