BERLIN—Germany’s Silvana Koch-Mehrin stepped down as vice president of the European Parliament on Wednesday, becoming the second prominent politician to have fallen victim to accusations of plagiarizing academic papers.

Heidelberg University has said it is investigating Koch-Mehrin’s doctorate for plagiarism and is expected to make a decision by the end of May or early June.

Her resignation comes shortly after popular Defence Minister Karl-Theodor zu Guttenberg stepped down after a scandal that ended in him admitting to copying part of his doctoral dissertation.

The Guttenberg scandal prompted a group of anonymous Internet activists to examine doctoral dissertations of politicians for plagiarism on a public website, the source of allegations against the 40-year-old Koch-Mehrin.

Koch-Mehrin, a well-known member of the junior coalition party the Free Democratic Party (FDP), said in a statement she had also resigned from the party’s board and as chairwoman of the FDP in the European Parliament.

The move comes as a further blow to a party already in disarray. This week, the FDP ousted its parliamentary floor leader in a shakeup aimed at reviving its flagging fortunes.

Last month, turmoil in the party forced its leader Guido Westerwelle to step aside and a party congress starting on Friday in Rostock is expected to boil over. Trouble in the party could hurt Chancellor Angela Merkel’s coalition.

Bayreuth University has said Guttenberg, once the brightest star in German politics, deliberately cheated to get his law doctorate, of which he has now been stripped.