The headteacher at Pimlico academy, the London secondary school at the centre of protests over allegations of race discrimination, has resigned.

Daniel Smith announced that he had decided to step down on Tuesday afternoon. The resignation comes after hundreds of students at the school took part in a demonstration at the end of March over changes to the curriculum, uniform policy and the siting of a union flag outside the academy building.

In an email sent to staff, Smith wrote that he had informed Future Academies – the trust which runs the school – of his intention to step down as principal of the academy earlier this term.

“The trust have agreed to this and I will leave the academy at the end of this half-term,” he said.

Smith informed staff that Tony Oulton, the current vice-principal of the school, would take up the post of acting principal from the start of next term.

“I will be working with Tony to ensure a smooth transition in the coming weeks. I would like to take this opportunity to thank you for your ongoing commitment to our students in what has been the most challenging of times,” he added.

In March the Guardian exclusively revealed that students, parents and some staff at the central London academy were angry over hairstyle and hijab rules, and changes to its history curriculum. The school then became the focus of protests after staff and students raised objections to its leadership style and policies.

Sir Michael Wilshaw, a former chief inspector of schools in England, said this month that he had been asked to visit the school to offer his expertise to Smith.

The National Education Union (NEU), which represents teachers at the school, has previously passed a motion of no confidence in Smith. Martin Donohue, the senior regional officer of the NEU’s London branch, said that in a ballot, members at the school had overwhelmingly voted in favour of strike action over what was described as an “unacceptable” management style. The school leadership has been accused by some staff of communication failures, unreasonable demands and failing to provide a safe working environment.

Lucinda Merritt, whose teenage son and daughter attend the school, and who has previously said she had been left devastated by recent events, welcomed the resignation.

“This decision should have been made months ago before all the emotional stress and the teacher resignations, but better late than never,” she said.

“I hope that the board of governors can now take the time to carefully consider who they appoint as principal, and really take note of the call for better representation in the senior leadership team and appoint a principal that is from the same world as the students so incidents like the uniform policy never happen again,” she added.

A teacher at the school, who wanted to remain anonymous, welcomed the resignation but raised concerns about the trust’s priorities.

“Even in his final moments in the school, Daniel Smith managed to bungle his exit. Mere days after briefing the staff on his upcoming priorities and hours after negotiating contracts with new and returning staff, he announces his resignation in an optional meeting and via a vague and non-committal email,” they said.

They added: “Staff are feeling positive, but this is but one battle in an ongoing war against the trust’s jaded priorities.”

Future Academies was set up by John Nash and his wife, Caroline, in 2006. They both maintain prominent roles in the organisation.

Lord Nash was a Conservative donor before being appointed as an education minister in 2013 in charge of academisation and being given a peerage.

Lady Nash, a co-chair of governors of the school, as well as chair of governors at two primary schools in the academy chain, is a former stockbroker.

The trust’s Curriculum Centre describes her as the “leading force in curriculum development across the trust”. It states that she has overseen the development of the new KS3 curriculum at Pimlico academy. Her biography does not list any teaching qualifications.

In a letter to parents, the couple wrote that Smith would leave his position as principal on 31 May this year.

“Mr Oulton will write to you shortly to introduce himself and outline his plans for the rest of this year,” they added.