The US president tweeted he was surprised that the company had become “the first to wave the white flag”, adding: “I fought hard for them.”
Harley-Davidson earlier said making bikes for the European market would be transferred to other countries.
The EU tariffs are a response to new US duties on steel and aluminium imports.
White House press secretary Sarah Sanders also told reporters at a briefing on Monday that the EU was “attempting to punish US workers with unfair and discriminatory trade policies”.
“President Trump will continue to push for free, fair and reciprocal trade, in hopes that the EU will join us,” Ms Sanders said.