Flights resumed at Cologne-Bonn and Dusseldorf airports on Tuesday, after workers returned from 24 hours of industrial action over pay.
At Düsseldorf airport, the strike ended at around 3 am (0200 GMT), said Verdi spokesman Peter Büddicker.
He did not expect any further restrictions for passengers.
At Cologne-Bonn airport, staff resumed work at 6 am, according to a spokesperson, who added there could be delays while backlogs cleared.
Almost every flight was cancelled at the airports on Monday, due to the one-day strike called by the Verdi and Komba trade unions. While 136 departures and arrivals planned in Cologne-Bonn, only two took place - a flight to and from Vienna.
The airport would otherwise have expected around 15,000 passengers on Monday.
The strikes are part of larger industrial actions amid negotiations for public sector employees at the federal and local levels, as well as the nationwide negotiations for aviation security employees.
Unions are demanding 10.5% more income, or at least €500 more per month.
