"The seriousness of this information, although it has not been proven, led me to present my resignation," said Esperanza Aguirre, 64, PP head in Madrid and a former education and culture minister under then premier Jose Maria Aznar.
Police on Thursday searched the headquarters of acting Prime Minister Mariano Rajoy's party and industrial group Villar Mir as part of a probe into allegations of irregular funding detailed in documents by a former deputy PP head in Madrid, Francisco Granados.
She was questioned Friday in another scandal involving alleged embezzlement by members of the Madrid chapter of the party, whose image has been tarnished by repeated graft scandals during its four years in power, as ordinary Spaniards suffer amid the country's prolonged economic woes.
Aguirre, who served as head of the regional government of Madrid between 2003 and 2012, has not been charged with any misdemeanour but was called to testify at a commission of inquiry created in October by the regional assembly to probe alleged wrong-doing in Madrid.
PP members are also due to be questioned by a judge over how computer hard drives of r party treasurer Luis Barcenas, who is in jail for embezzlement, were wiped clean before investigators were able to see them.
Corruption has fueled the rise of two new parties, Podemos on the left and market friendly Ciudadanos on the centre-right, and cost the PP votes in December elections which it won but without the absolute majority it got in 2011 polls.