At the height of the coronavirus pandemic, Susana Baez would begin her shift at 1 a.m., scrubbing trash, vomit and human excrement from subway cars.

She and her team, a largely immigrant work force contracted by private companies to clean New York City’s subway stations and train cars, often had to work without enough safety equipment, like gloves, she said. Many contracted Covid-19 on the job.

“It was trauma,” Ms. Baez, 53, said in Spanish about the job, which she performed from 2020 to 2023, when her contract abruptly ended.

Now, Ms. Baez and more than 450 other subway cleaners will split $3 million in back pay, after a multiyear investigation by the city comptroller found that they were grossly underpaid.

The workers, who were employed by two private cleaning companies, earned around 25 percent less than they were owed, said Brad Lander, the city comptroller. His office sets the prevailing wage, or the typical rate, for certain types of public work.

The cleaners made $16 to $18 an hour on average in the first years of the pandemic, without supplemental benefits, when $20 to $21 an hour was standard, Mr. Lander said. Minimum wage at the time was $15 an hour.