The clashes took place just before the reality TV star opened a branch of her Millions Of Milkshakes shop in the Gulf kingdom.
Protesters chanted “God is Great” near the shopping complex in Riffa, some 20km south of the capital Manama, but the demonstrators were cleared before the celebrity appeared.
The 32-year-old had previously posted glowing remarks about Bahrain on her Twitter account, calling it “the prettiest place on earth”. The message was re-tweeted by Bahrain’s foreign minister.
Her trip had sparked anger among Islamist legislators earlier in the week.
They submitted an urgent proposal at the end of a parliamentary session where they referred to her as “an actress with an extremely bad reputation”, according to the Gulf Daily News.
But the motion was dismissed because other MPs quickly left the chamber.
The furore did not seem to affect Kardashian, who described her visit to Bahrain as an “amazing trip”.
Kardashian was embroiled in a controversy two weeks ago after she posted Tweets first praying for Israel and then Palestine – leading to a backlash from her fans.
She later deleted the comments and issued a statement apologising for causing any offence.