Claire Bassett is to leave the Electoral Commission after a three-year stint as chief executive during which the regulator contended with the growth of online campaigning, investigated pro-Brexit campaigns for breaking electoral law and fined the Conservatives for busting spending limits in the 2015 general election.

Bassett will leave the chief executive role at the end of the year. Under her watch, the regulator warned that British democracy “may be under threat” and called for a raft of new legislation to clarify who is paying for online political campaign material, set new restrictions on who can give to political causes, and substantially increase the level of fines against campaigns that break the law.

The commission came under scrutiny for the way it dealt with claims of overspending during the EU referendum. Following several lengthy investigations, it concluded this summer – almost two years after the vote – that both Leave.EU and Vote Leave had broken electoral law.

The commission issued fines and reported individuals to the police for further investigation, but Bassett had already said that the maximum £20,000 fine available to her organisation, set by parliament, meant the penalties imposed were seen by campaigns as a “cost of doing business”.

Both pro-Brexit campaigns accused the commission of bias and politicising what until recently had been an important but largely obscure organisation. Leave.EU’s Arron Banks described it as a “Blairite swamp creation”.

Last year Bassett used a letter to the Guardian to emphasise that her organisation’s role was “to ensure transparency on where money is being spent to influence voting, rather than to stop campaigning”. “Indeed, the health of our democracy relies on the ability for candidates, parties and non-party campaigners to engage with voters in ways that voters find accessible.”

Bassett will move to a job running the new Trade Remedies Authority (TRA), which was created to protect British industry from unfair trading practices after the UK leaves the EU.