Microsoft chief executive Satya Nadella has been named chair of the software company, ending two decades of separation between the positions, amid questions about the board’s handling of an investigation into co-founder Bill Gates.

The appointment made Nadella only the second person to hold both chief executive and chair titles in the company’s 46-year history. Gates occupied both roles until stepping back as chief executive in 2000, though he remained as chair until 2014 and still acts as an adviser to Nadella.

Microsoft sought to paint the boardroom transition as a natural extension of Nadella’s seven-year leadership. The move had been under informal discussion between the chief executive and former chair John Thompson since late last year, according to a company spokesperson. It was also approved at the board’s regular June meeting, when it makes any boardroom changes ahead of its financial year-end that month, the spokesperson said.

However, it also came at a moment when the board is under the spotlight over its handling of Gates’s departure as a director last year. He left after Microsoft’s directors — including Nadella — started an investigation into what the company recently called a “concern . . . that Bill Gates sought to initiate an intimate re­la­tion­ship with a com­pany em­ployee in the year 2000”.

The investigation only became public a month ago, after Gates and his wife Melinda announced their intention to divorce and US media reported allegations of sexual approaches to women at both the software company and the couple’s charitable foundation. Through a spokesperson, Gates has denied he left the board due to the company’s investigation.

At the time, he said that he was leaving “to dedicate more time to philanthropic priorities”. Microsoft refused to say on Wednesday whether its board investigation had concluded, or whether it had allowed the matter to drop after Gates stepped down.

Thompson, who has acted as chair since 2014, had moved back to the position of lead independent director that he held previously, the company said.

Gates has been a continual presence at Microsoft in the more than two decades since he stepped down as chief executive at the height of US antitrust action against the software group.

After handing over the chair’s title in 2014, he continued to spend a third of his time at the company advising Nadella, with the rest split between the Bill & Melinda Gates Foundation and his private investment group. Since leaving the company in the wake of the board investigation, he has continued as an adviser to Nadella while spending far less time on Microsoft work, according to the company spokesperson.