West, known as Ye, performed at the Gelredome stadium in Arnhem before a crowd of 40,000.
The concert went ahead despite calls for cancellation and a small demonstration by the Jewish organization CIDI (Centrum Informatie en Documentatie Israel), which displayed placards bearing antisemitic quotations attributed to the artist.
CIDI director Naomi Mestrum said the organization was not satisfied with West's public response to the controversy.
'I know that his fans are probably coming for the music, but we cannot look away from the Jew-hatred that he has spread widely in the past,' she said.
'If you really want to make amends, you have to (make) more than just an apology on Twitter.'
An Amsterdam court had previously ruled that the shows did not pose a threat to public order, allowing the concerts to proceed.
Some fans outside the venue said they chose to separate the artist's public statements from his music. 'I'm not supporting all of those things he said, like it's really controversial,' said Loes Snyers, a 20-year-old Belgian student.
'But for me, I really don't care about the backlash of all the bad stuff artists do; I really focus on the music.'
West has denied being antisemitic, attributing remarks he made, including comments glorifying Nazi leader Adolf Hitler and a song titled 'Heil Hitler,' to his bipolar disorder.
West's European tour has faced significant disruption. Concerts were canceled in the United Kingdom, France, Poland, and Italy.
Mestrum noted that other countries had 'drawn a moral line' in rejecting the artist. 'We are not happy with the fact that he gets such a huge stage here in the Netherlands, where other countries around us have drawn a moral line and rejected him,' she said.
West is scheduled to perform in the Albanian capital, Tirana, on July 11 and in Prague on July 25.