Protesters say the Transatlantic Trade and Investment Partnership (TTIP) will lower European standards on food and environmental protection, and could lead to outsourcing and job-losses.
Supporters of the deal say it promises to lower tariffs and promote growth.
The demonstrators are also protesting against a similar deal with Canada.
There were large crowds carrying flags and banners in seven German cities, including Berlin, Munich, Hamburg and Frankfurt, all braving cool and wet weather.
"I want us to get rid of TTIP and for European social and environmental standards to be respected, maintained and improved," said Peter Clausing in Berlin.
Many demonstrators think the deal would lead to exploitation of people by businesses on both sides of the Atlantic.
"It will be the enterprises and banks that will have power over people worldwide", said Tobias Kuhn. "That is a no-go. People need to know that and we will protest until there's no chance of that happening anymore."
The EU and the US began negotiating the trade deal in 2013, aiming to create the world's biggest free trade market with 850 million consumers.
A new round of talks is due to start in October, and President Obama says he wants the deal to be concluded before he leaves office in January.
A similar but smaller trade deal between the EU and Canada, called the Comprehensive Economic Trade Agreement (CETA), is due to be signed in October.
- See more at: http://www.sigmalive.com/en/news/international/148742/protesters-demand-end-of-ttip-all-over-germany?#.dpuf
