Employees at Amazon’s centres in Leipzig, and Bad Hersfeld, Hesse, walked out at 5.30am, workers' union Verdi's spokesman Thomas Schneider confirmed.
Many braved bitterly cold weather to stage dawn protests outside their offices.
He added that they would be calling on staff working the later shift on Monday to also strike, and that the action could last a couple of days.
In the Bavarian Amazon offices in Graben around 50 employees gathered at the front door to stage a protest – in the hopes of rousing up more staff to strike with them as they came to work, Spiegel online news site reported.
“Amazon is characterized by low wages, constant pressure to perform and temporary contracts,” said Verdi board member Stefanie Nutzenberger.
The company has been consistently rejecting requests for higher wages for its 9,000 German employees, sparking a series of strikes since the summer.
The firms says its employees are paid well compared to others in Germany’s logistics sector.
There is also supposed to be, according to Verdi, a strike in front of Amazon's Seattle base on Monday in a show of solidarity. German representatives have flown over to take part.
Verdi is planning further action on Tuesday in the town of Werne, North Rhine-Westphalia.