The Greens' candidate, Sibylle Keupen, won more than two thirds of the vote in Aachen, on the border with Belgium and the Netherlands.
In Bonn, the former German capital, Green party national lawmaker Katja Doerner ousted the incumbent mayor from Chancellor Angela Merkel's Christian Democrats.
In the industrial city of Wuppertal, Greens candidate Uwe Schneidewind won the runoff against the center-left Social Democrat incumbent.
Merkel's party won runoff votes in Cologne and Duesseldorf.
The Greens were the only party to make big gains in the state's municipal elections two weeks ago, almost doubling their share of the vote compared to 2014 and coming third.