Ms Metsola, 43, has a record of being anti-abortion, but has billed herself as pro-LGBT rights.
The Maltese national takes over the role from David Sassoli, 65, who died last week after a serious illness.
She is one of three women in the top EU jobs, along with the heads of the European Commission and Central Bank.
But taking questions from journalists on Tuesday, she was asked more than once about her views on women's reproductive rights.
She's been criticised for her voting record on the issue and, in 2015, joined other Maltese MEPs in saying they were "categorically against abortion".
A predominantly Catholic country, Malta is the only EU member state to have a complete ban on abortion.
However, Ms Metsola has insisted she will represent the European Parliament's view on sexual and reproductive health, rather than her own.
The parliament has, she said, "repeatedly called for these rights to be better protected".
"My position is that of the European Parliament."
A member of the centre-right European People's Party, she is a lawyer by training. She's long been part of the Brussels bubble although addressing MEPs she urged the EU to "burst through it".
Her previous jobs have included acting as legal adviser to British politician Baroness Ashton, who was then the EU's top diplomat.