Walkouts by cabin staff grounded at least 58 flights on Wednesday, a labour union said, and travellers geared up for more disruption ahead of a planned strike by rail workers.
The six-hour strike affected Lufthansa's main hub Frankfurt as well as Berlin and follows similar action last week as the UFO union presses demands for a 15 percent wage increase.
A spokesman for the German carrier, which has offered a 10 percent raise, could not say how many flights were disrupted.
At the same time, labour unions Transnet and GDBA, which represent 130,000 workers, have called a one-day strike on Thursday over pay and working hours at Deutsche Bahn DBN.UL, Germany's dominant rail company.
Union leaders said action would be limited to selected areas and there were no plans to "paralyse the entire nation".
German train drivers brought most of the national network to a standstill in a series of strikes in 2007.
Lufthansa's personnel chief Stefan Lauer called on UFO "not to cause customers any further damage, given the current economic situation and declining passenger and freight figures".
Lufthansa cancelled 44 flights last Friday after a three-hour strike which affected hundreds of passengers on domestic and European flights.
Last July, strikes by ground staff, cabin crew and regional pilots curtailed flights.
The deal to settle that dispute added about 100 million euros ($130 million) to annual costs, Lufthansa said.
Lufthansa in October cut its 2008 operating profit goal to 1.1 billion euros, from a previous estimate of about 1.38 billion.