What should a Muslim do with the profits from selling shares of a company that was later discovered to be involved in riba (usury)? Should he dispose of all the profits, or only the portion of the profits derived from riba?

If the company's activity is permissible but it has some usurious dealings, and you sell the shares, you are only required to disburse the unlawful portion of the profit gained. Some scholars are of the opinion that it is permissible to benefit from the entire profit if you were unaware of the impermissibility at the time of purchase, citing the words of Sheikh Ibn Uthaymeen that whoever was unaware of the impermissibility or was misled by the fatwa of a scholar, what he has taken is his, in accordance with the verse: "So whoever receives an admonition from his Lord and desists, he may have what has already passed, and his affair is left to Allah." As for one who is aware of the impermissibility, he should dispose of the usury through charity or other charitable causes.