He developed a program that is used by the organization in riba-based transactions

If the role of the bank in this transaction is limited to financing purchases in return for interest, then this transaction is clearly riba-based. But if the bank buys the item in a real sense, then sells it by installments to citizens – for a greater price than if it were to be paid on the spot – then there is nothing wrong with that, so long as the bank does not increase the price of the item again if the customer delays payment of any installment.

If the transaction is unlawful and you were aware of that at the time when you were developing the program, then you have helped with riba and your work is haraam, and what resulted from it of payments is also haraam; you have to repent to Allah, may He be exalted, but you do not have to do anything about the money that you spent before repenting. As for what is left of that money, you must get rid of it by donating it to charitable causes.

See question no. 78289.

If you are unaware of the prohibition, or of what the organization was going to do of unlawful transactions, then there is no sin on you, and you can make use of the fee that you received, both what you have already spent and what you have not yet received.

It says in Fataawa al-Lajnah ad-Daa’imah (33/14): I want to ask you about a fatwa from one of the scholars that is widely known among the people, which says that if a person earns money by making alcohol or selling it, or selling drugs, and he repents to Allah, may He be glorified and exalted, then the money that he earned by making or selling alcohol, or selling drugs them is halaal. As many seekers of knowledge are wondering about this, we would like to ask you about it.

Answer: If at the time of earning that haraam money he was aware of the prohibition, then it does not become permissible to him by means of his repentance; rather he must get rid of it by spending it on charitable causes and good works. End quote.

Shaykh Ibn ‘Uthaymeen (may Allah have mercy on him) was asked about the repentance of someone who worked in a riba-based bank and how he should repent. Should he get rid of all the haraam wealth that he earned, or what should he do? Because I have read different views from the scholars. Some of them said that he should get rid of whatever he possesses of haraam wealth if he was aware of the prohibition, but if he was not aware of it then he does not have to get rid of anything. Some of them say that he may keep everything that he had in his possession before repenting, so as to make it easy for him to repent. And some of them say that he should get rid of all riba, because Allah says (interpretation of the meaning): “you may have your principal [capital]” [al-Baqarah 2:279]. What is the ruling that is supported by the evidence, may Allah reward you, and will make it easy for our brothers to get rid of everything that is unlawful?

Answer: What appears to me to be the case is that if he did not know that this is haraam, then he may keep everything that he earned and he does not have to do anything, or if he was deceived by the fatwa of a scholar who says that it is not haraam, then he does not have to get rid of anything. Allah, may He be exalted, says (interpretation of the meaning): “So whoever has received an admonition from his Lord and desists may have what is past, and his affair rests with Allah” [al-Baqarah 2:275]. But if he was aware (of the ruling), then he must get rid of the riba by giving it in charity, or by building mosques or repairing roads and the like.

End quote from al-Liqaa’ ash-Shahri (11/67).

This is applicable to working with riba and other kinds of haraam work.

May Allah help us and you to obey Him and do that which pleases Him.

And Allah knows best.