Restaurant Group, which owns both chains, announced on Friday that it would sell or close 33 outlets across the UK.
It confirmed that Frankie & Benny's in Londonderry, Coleraine and Ballymena would close.
The Chiquito store in Belfast's Victoria Square is also set to shut.
Restaurant Group said they had suffered a "challenging trading period".
It said its Frankie & Benny's chain had "suffered due to insufficient focus on value, unsuccessful menu development and poor operational execution".
Those outlets had lost customers after "significant price increases and the removal of popular value offers".
The company said it was "taking action" to change this, adding it would stick with the Frankie & Benny's brand as it remained "relevant and popular".
Up to 100 jobs are at risk with the closure of Frankie & Benny's and Chiquito restaurants in Northern Ireland.