Obama's trip -- to open an industrial technology fair in the northern city of Hanover and hold talks with Chancellor Angela Merkel and other European leaders -- was intended to lend momentum to flagging efforts to see the world's biggest trade pact finalised this year.
In an interview with German newspaper Bild ahead of the visit, Obama underscored his belief that the deal will strengthen trade and create jobs.
But the Trans-Atlantic Trade and Investment Partnership (TTIP) has run into major opposition, not least in Europe's top economy Germany, where its foes have raised the spectre of eroding ecological and labour market standards and condemned secrecy shrouding the talks.
Amid a heavy police presence, one banner reading "Don't give TTIP a chance" featured the image of a bull tagged "privatisation" and a cow branded "democracy".
A mock coffin lay on the ground emblazoned with the words "Democracy killed by money" and "Here lies democracy".
"We are not demonstrating against Obama but against TTIP," said the head of one campaign group, Campact, Christoph Bautz.
A similar protest in October in Berlin drew up to 250,000 people, according to organisers, signalling an uphill battle for the deal's passage.
In a video podcast, Merkel insisted Saturday that TTIP would not ride roughshod over citizens' rights or interests.
"We don't want people to have the impression that something is being hushed up here, or that norms are being undermined. The opposite is true," she said.
In what she called a "win-win situation", Europe and the United States had the opportunity to agree on environmental and consumer protection principles that, due to the massive size of the market, "could set global standards".
However, US Trade Representative Michael Froman told the German business daily Handelsblatt on Friday that if the negotiators fall short, "there will be real doubts about whether we will ever get this agreement through".
The Hanover meeting comes just before a 13th round of TTIP negotiations starts Monday in New York.
But scepticism in the face of those arguments is growing in Germany, and Economy Minister Sigmar Gabriel admitted this week: "It is possible that TTIP will fail.
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