Henry Mulyana voluntarily shut down his SoldatenKaffee last year after media reports exposed his swastika-clad establishment, prompting death threats and accusation of inciting racial hatred.
Following the closure, his lawyer told AFP that Mulyana would later reopen his business with a broader World War II theme and said he would remove all swastikas.
But at the opening on Saturday, three huge iron eagles bearing swastikas were on display, as were WWII propaganda posters bearing the Nazi symbol.
Several young men attended the opening dressed in military outfits, including one bearing a swastika on his arm, and some posed for photos as prisoners of war in a mock interrogation room.
Mulyana has tried to broaden his cafe's theme by including images of other wartime figures to his collection, including Winston Churchill and Josef Stalin.
"From the beginning I have said that the SoldatenKaffee is not a Nazi cafe. This cafe's theme is World War II," Mulyana told reporters at the reopening in the western Java city of Bandung.
"All aspects of the SoldatenKaffee are legal. We have a lot of customers from Europe and they don't have a problem with the World War II theme, because it is seen here from a historical perspective," he said.
Ninety percent of Indonesia's 250 million people identify as Muslim, making the country home to the world's biggest Islamic population.
The SoldatenKaffee ("The Soldiers' Cafe") was named after the popular hangout for soldiers in Germany and occupied Paris during World War II and had operated in Bandung for three years until it was exposed in English-language media.
The reports prompted fierce criticism from abroad, particularly from Jewish organizations, including the LA-based Simon Wiesenthal Center, which expressed its "outrage and disgust" and called for the cafe's closure.
That Mulyana is allowed to keep his cafe open sits in stark contrast to attitudes in Europe, where several countries have criminalized promoting Nazi ideology and Holocaust denial.
The Jewish population in Indonesia is tiny, but historians have blamed poor schooling in the country for the lack of awareness and sensitivity of the Holocaust.