Saudi's index rose as much as 0.8% at the open before changing tack to trade 1.1% lower. Al Rajhi Bank dropped 2.2% and Riyad Bank 4.4%.
A second batch of Saudi shares will be added to the MSCI emerging markets index on Wednesday after the country's stocks were first included in the index in May.
Three of an eventual five tranches of Saudi stocks have also been added to the FTSE emerging-market index this year.
The inclusion of Saudi stocks in the indexes has attracted billions of dollars from foreign investors, who have been net buyers every month this year, sending the Saudi index up nearly 20% at its peak in May.
But regional geo-political tensions and the global trade war have since reduced the year-to-date gains to 4.3%.
The Abu Dhabi index added 0.9% to the previous session's gains, when it broke a three-day losing streak. Emirates Telecom gained 1.6% and First Abu Dhabi Bank edged up 0.4%.
In Dubai, the index was up 0.5%, led by financial stocks. Dubai Islamic Bank and Emirates NBD Bank added 1.2% and 0.4% respectively.
Qatar's index was flat. The Gulf's largest lender Qatar National Bank lost 0.4%, offsetting gains in blue-chip petrochemical maker Industries Qatar, which was up 0.4%.