The bank's pay plan was voted down by 51.9 per cent of its investors, with 48.1 per cent voting in favour.
Deutsche has weathered several storms during the last 12 months, with the result that its share price has halved over the past year.
In the last six months, it has announced a management cull and a major restructuring, revealed in October, and in December it was linked with a $10bn (£6.8bn) Russian money laundering scandal.
Chief executive officer John Cryan was still able to hold on to shareholder support however, with 98.5 per cent voting in approval of his performance.
He took over the role last summer, after Deutsche's previous bosses, Anshu Jain and Jurgen Fitschen, were forced to resign following months of unrest at the firm. Fitschen stayed on as co-chief exec but has now stepped down, leaving Cryan as sole chief executive for the first time.
Speaking at the AGM, Cryan warned shareholders that Deutsche is facing further significant legal charges this year, having already set aside €5.4bn (£4.1bn) to settle pending litigation.
The bank is dealing with claims filed by individuals, companies and regulators relating to mis-selling of subprime loans, manipulation of foreign exchange rates or gold and silver prices, and the rigging of borrowing benchmarks Libor and Euribor.