Boston was finally about to get an MBTA board seat. Instead, it was another casualty of the Legislature’s 11th-hour scramble.

The change had seemed all but assured after a version earned approval from the state House, Senate, and governor

Boston Mayor Michelle Wu commutes on the Orange Line.David L. Ryan/Globe Staff

On this, everyone seemed to be in agreement: Boston should get a seat on the board of the MBTA.

Mayor Michelle Wu had been pushing for it for years, even before she was elected to lead the capital city. The Massachusetts House passed it, the Massachusetts Senate agreed to it, and even Republican Governor Charlie Baker signed on to the concept of granting Boston some official oversight over the transit agency.

And yet the Legislature ended its formal session on Monday without taking the last vote needed to finalize the change to the board, leaving Boston without any formal authority over the regional transit system its residents rely on. The board seat, which had been included in the state budget but stalled after Baker tweaked the provision, became one more casualty of the all-night, eleventh-hour scramble on Beacon Hill, where last weekend legislators passed major initiatives and let others die while most of their constituents slept.

It’s a setback, though perhaps a temporary one, for transit-focused Wu, who ran on making the T fare free and whose Orange Line commute has become a core piece of her political identity. And it comes at the end of a session that saw Wu secure significant funding for the city, but also fail to pass a top legislative priority related to housing, in an early indication that this mayor, like her predecessors, may struggle to gain influence on Beacon Hill.

The Legislature could still grant Boston a seat on the board, either when it reconvenes formally in January or perhaps sooner, during what’s known as an informal session. But passing substantive measures during those informal sessions carries major risk: Just one state lawmaker has the power to sink even a popular provision.

Wu said in a statement Monday that “it would be a major step forward for Boston to have a direct voice in shaping and supporting the decision-making” at the Massachusetts Bay Transportation Authority.

“We’re hopeful that this can be a part of conversations the Legislature has in the coming weeks and months,” she added.

For now, though, the Legislature’s inaction scuttles any immediate plans Wu had for the beleaguered transit system, which in the past few months alone has witnessed multiple derailments, an Orange Line fire that forced passengers to climb out of train windows, a battery “failure” that experts say was likely an explosion, and even the death of a passenger, who was dragged by the Red Line after getting his arm caught in a train door.

In the wake of those problems and in apparent anticipation of greater control, Wu had recently begun to telegraph her preferred plans for the system.

Discussing safety maintenance during a radio interview last week, Wu said the T “can no longer tolerate tinkering around the edges or just trying to fix things up here or there.”

“It is time to talk about just ripping the Band Aid off and taking drastic action,” she added during a July 25 interview on WBUR’s “Radio Boston.” Specifically, she said, the MBTA should shut down major sections of the Orange Line for a sustained period of time in order to make crucial repairs, “rather than just trying to do a little bit of track here or there.” Boston would be prepared to help manage the disruption, she said, devoting street space for shuttle buses to carry commuters.

It was an idea Wu said she had communicated to the MBTA, and one that aligned with the position of federal officials, who have been conducting a safety investigation into the T.

Just days after that radio interview, the MBTA abruptly announced it would postpone planned maintenance on the Orange Line in order to broaden the scope of the work.

Wu has waged a years-long campaign to get Boston a seat on the MBTA board. In 2019, the then-city councilor wrote a Globe opinion piece calling for “changed governance.” Since April, she has sent legislative leaders three letters calling for a board seat for Boston and another for neighboring municipalities served by the T.

Both seats had seemed all but assured as recently as last week, after the Democrat-dominated Legislature approved them as part of the $52 billion state budget. But on Thursday, Baker tweaked that provision in an amendment that would have given the governor slightly more control. Instead of allowing the mayor to directly appoint a board member, Baker’s version would have allowed the governor to select from three nominees put forward by Boston’s mayor. The Massachusetts House on Saturday approved Baker’s version, but the state Senate did not take it up for a vote before the legislative session ended Monday.

A spokesperson for Senate President Karen E. Spilka did not return requests from the Globe for comment.

As the session came to a close Monday, Boston could celebrate other victories: securing $110 million for homeless shelters and millions more for summer jobs for at-risk youth and Boston Fire Department training, among other priorities.

But perhaps more notably, the Legislature did not vote to allow Wu to levy a new tax on high-dollar real estate transactions in Boston to raise money for affordable housing. Decades-old state laws prevent Boston and other municipalities from enacting even straightforward local ordinances without state signoff, leaving them at the mercy of the Legislature. The city-state power imbalance is in part the relic of ethnic strife between the Irish, who earned increasing political power in Boston at the start of the 20th century, and the Brahmins, who consolidated their power on Beacon Hill as they saw it slipping away in local government. That legal structure has made getting permission for local measures an uphill battle.

Wu is not the first Boston mayor to send the so-called transfer tax to the Legislature, nor the first to see it die. Former mayor Martin J. Walsh, himself a former state lawmaker, could not get the proposal through the Legislature, and other localities have been unsuccessfully pushing similar proposals for years.

If the transfer tax was a test of Wu’s political influence on Beacon Hill, she didn’t pass it in the first go-around. But allies said the mayor may have more success in future on both the transfer tax and the MBTA board seat. When Wu proposes legislation next year, she can do it at the start of the session instead of midway through, and she will do so under a new governor, likely a Democrat more aligned with her positions. Strong relationships with Massachusetts leaders are crucial for Wu, as many of her top priorities depend on state approval.

State Senator Lydia Edwards, a Wu ally and Democrat who represents East Boston, said the changes to the MBTA board could earn approval as soon as this year and the mayor may see more of her proposals become law in future sessions.

Wu had a “good, but not great year” on Beacon Hill, Edwards said.

But “the real test as to how influential she’s going to be,” will be next year, she added. “A lot of things will be aligning for her to really set a more aggressive pace in the State House that she really couldn’t do this time.”