This was the latest fallout from increased scrutiny of Angola's former first daughter, a highly divisive figure in her home country, where she is nicknamed "the Princess" after amassing a fortune estimated at more than $2 billion during her father Jose Eduardo's decades-long presidency.
A spokesman for Portugal's prosecutor's office said it would investigate reports about dos Santos while the central bank said in a statement it had asked Eurobic bank about transfers between Angola and Dubai, following the same reports.
Both institutions said they would take appropriate action if needed, without giving any details.
The central bank statement, the prosecutor's office and Eurobic all referred to hundreds of thousands of files about dos Santos dubbed the "Luanda Leaks" - obtained by the International Consortium of Investigative Journalists (ICIJ) and released by several news organisations on Sunday.
The media reports focused on alleged financial schemes used by dos Santos to build her business empire, including transfers between Angola and Dubai.
Dos Santos, who holds a 42.5% stake in Eurobic indirectly via two entities and does not sit on the board, said on Sunday that allegations made against her were "completely unfounded."
Eurobic, which was already under investigation from the central bank over its links to dos Santos, said it decided to end its business relationship with all entities controlled by the billionaire.
The bank's board of directors decided in a meeting on Monday to "terminate the commercial relationship with entities controlled by the universe of the shareholder Isabel dos Santos and people closely related to it."
However, Eurobic did not say what that would mean for its own relationship with dos Santos, its main shareholder. It could not immediately be reached for any additional comment.
Angolan authorities froze dos Santos' assets in the African country in late December following allegations by prosecutors that she and her husband had steered payments of more than $1 billion from state companies Sonangol and Sodiam to firms in which they held stakes.
Dos Santos and her husband have denied any wrongdoing.
In Portugal, dos Santos holds significant stakes in several important firms, including telecoms company NOS.
Portugal's Sonae, which partners with dos Santos in NOS, said in statement late on Monday that it was following the situation with "attention and concern, especially given allusions made to several non-executive members of the board of directors of its subsidiary NOS."
A Sonae spokesman told Reuters Sonae has total confidence in NOS. Dos Santos and Sonae each own 50% of holding company ZOPT-SGPS, which controls 52.15% of NOS.
By Sergio Goncalves and Catarina Demony