Begoña Gómez, the wife of Spain’s prime minister, Pedro Sánchez, has been charged with embezzlement, influence peddling, corruption in business dealings and misappropriation of funds at the end of a two-year investigation by a judge in Madrid.

Gómez, 55, has been accused of using her influence as the wife of the socialist prime minister to secure and manage a post at Madrid’s Complutense University, and of using public resources and personal connections to further her private interests.

The judge, Juan Carlos Peinado, has also charged Gómez’s personal assistant, Cristina Álvarez, and a businessman, Juan Carlos Barrabés, in connection with the case.

All the accused have denied wrongdoing.

The investigation into Gómez was triggered by a complaint from Manos Limpias (Clean Hands), a self-styled trade union with far-right links that has a history of using the courts to pursue those it deems a threat to Spain’s democratic interests.

Sánchez had repeatedly dismissed the case against his wife as a baseless and politically motivated smear. The prime minister has accused his political and media opponents of pursuing his family and has also openly questioned the impartiality of some members of the judiciary.

In his 39-page ruling, Peinado suggested that “certain public decisions favourable to the [university chair], which could have been obtained through a unique exploitation of her relational position, had been taken since Gómez’s husband became secretary general of the Spanish Socialist Workers’ party and, above all, since he became prime minister”.

The judge also said there was evidence of behaviour at the Moncloa palace – the prime minister’s office and official residence – that “seems more in keeping with that of absolutist regimes and which has, fortunately, been forgotten in our state over the years”.

The prime minister, who said last year “there’s no doubt that there are judges doing politics and there are politicians trying to do justice”, said he was confident justice would be served and his wife would be cleared.

“What I ask of the justice system is that it delivers justice,” Sánchez said during a visit to China on Tuesday. “That justice be served. And since I’m convinced that time will put everything and everyone in their place, I have nothing more to say.”

Peinado, who faces mandatory retirement as a judge in September, has given parties in the case five days to respond to his decision. The courts will then decide whether Gómez will face a jury trial.

The decision to formally charge Gómez comes at a fraught time for Sánchez as the prime minister’s younger brother, David, is due to be tried next month on charges of influence-peddling. According to another complaint from Manos Limpias, David Sánchez was handed a bespoke job by the socialist-led council of the south-western city of Badajoz in July 2017, when his brother was the national leader of the socialist party. He denies the charges.

Meanwhile, two senior former figures in Sánchez’s government are on trial for alleged corruption. The prime minister’s former right-hand man, the ex-transport minister José Luis Ábalos, is accused – along with his former aide Koldo García and the businessman Víctor de Aldama – of taking kickbacks on public contracts for sanitary equipment during the Covid pandemic. Ábalos and García, who deny all charges, are facing sentences of 24 years and 19 years respectively while Aldama, who has already admitted to his part in the alleged scheme, faces a seven-year sentence.