The school system soon marked a turning point. Graduation rates skyrocketed and dropout and suspension rates plummeted. Test scores saw historic growth. Enrollment and attendance in the city's schools showed steady growth.
And the former special-education teacher led the district into a settlement of a federal lawsuit that had been lodged against the system in 1986 alleging it failed to serve special-education students.
With the accomplishments, and the backing of a school board that granted him unprecedented autonomy to run the district as he saw fit, Alonso raised Baltimore's profile as a leader in urban education reform.
Polytechnic Institute senior Reginald L. Smallwood III said Alonso left a mark on students' lives by redesigning the discipline code and reducing suspensions and dropout rates.
"I have spoken with a lot of people who have said it's better than the previous system, and it keeps students focused and motivated rather than isolated," said Smallwood, 17, who is a member of the school board.
State Superintendent Lillian Lowery commended Alonso for developing "a very diversified portfolio of choice" for families and an inclusive teacher performance evaluation process, but she said his hallmark was negotiating the 10-year school construction plan.
"His areas of strengths have been many," she said. "He brought a level of accountability there that was much needed around student performance and holding people to high expectations to ensure that everyone has our children's best interest at heart."
Robert C. Embry Jr., president of the Abell Foundation, called Alonso's resignation "very sad."
"We were lucky to have him for six years. He'll be missed," Embry said. "By almost every objective measure, the school system is better off today than when he was hired. He's always been open to other people's ideas, non-dogmatic and evidence-based. It's hard for me to imagine a better superintendent."
Alonso will finish the school year and then move back to Weehawken, N.J., and begin a commute to the Harvard Graduate School of Education. He has been named a professor of practice — a title and position the school extends to those of national or international distinction "who have had a major beneficial impact on education practice or policy," according to the school system.
Alonso said previously that he'd hoped to stay in the district for 10 years. He told The Baltimore Sun at the outset of his tenure that if at any point he was prevented from making decisions that he believes are in kids' best interests, he would leave.
When he signed a new $260,000, four-year contract in July 2011, Alonso said his ability to be effective would determine how long he would stay in the city.
"Superintendents have short tenures," Alonso said at the time. "If I wanted to be a superintendent that lasts 10 years, then it'd be easy for me. That's not what I want to be.
"I want to last 10 years by doing what I think is right for schools and communities for as long as schools and communities agree that I'm the right person to do it, and that the direction I'm taking the district is the right one."
But as the schools chief renewed his commitment that year, the district started to stumble.
Test scores stalled, and a series of cheating scandals — found by the state to have taken place during the year the district's progress was most celebrated — cast a cloud over the success story.
Unprecedented turnover and pressure on school leaders soured Alonso's relationship with the city's principals union, which also challenged his decision to hold principals responsible for suspected cheating and which denounced the evidence Alonso had used to build some of the cases.
And in the past year, the school system has been embroiled in controversy over imprudent spending and financial mismanagement.
Among the issues: the system had paid $14 million in overtime over several years, with the top earner being Alonso's driver; credit card records showed employees at school headquarters had spent $500,000 with virtually no oversight; and the head of the IT department spent $250,000 to renovate his suite.
In addition, a state audit released late last year faulted the district for failing to collect millions of dollars in debt, overpaying dozens of employees in salaries and benefits, and paying $2.8 million in overtime without substantiating hours.