Praise be to Allah.
We put this question to Shaykh Muhammad ibn Saalih al-‘Uthaymeen, may Allaah preserve him, who replied as follows:
It is not permissible to work for this company unless he puts the condition that he will not have to deal with riba, meaning that he should not record anything having to do with riba.
This computer program runs calculations by pressing buttons, so the accounts for all budgets are done by pressing buttons. They are not recorded on paper, for example, so that he could record this and not record that. Everything is done by pressing buttons, including those that involve riba. It is not possible to separate between them.
To be on the safe side, he should not work there, and Allaah will send his provision. And Allaah knows best.