The US president and the Prime Minister will hold a delayed meeting in New York on Wednesday, as Ms Truss attends a United Nations summit.
She declined to discuss the protocol with France’s Emmanuel Macron a day earlier, and No 10 did not say if she will raise it with European Commission president Ursula von der Leyen.
But US national security adviser Jake Sullivan made it clear will discuss it “in some detail” with Ms Truss.
Ms Truss is pushing ahead with her controversial Northern Ireland Protocol Bill, that the EU and other critics say will breach international law by suspending elements of the agreement.
There have also been suggestions she could unilaterally trigger Article 16 of the protocol, to override parts of the agreement brokered as part of the Brexit divorce deal.
Mr Biden and Ms Truss will also meet after a tweet from the president sent just as the PM was discussing her economic policy, which said he was “sick and tired of trickle-down economics”.
“It has never worked,” he said.
The comments underlined the differences between the two leaders’ stances just as Ms Truss says she wants to foster closer ties with international allies.
The Prime Minister’s official spokesman said it was “ludicrous” to suggest Mr Biden was criticising UK policy, arguing each country is facing different economic challenges.
Mr Sullivan told reporters the president “will encourage the UK and the European Union to work out an effective outcome that ensures there is no threat to the fundamental principles of the Good Friday Agreement”.
“And he will speak in some detail to her about that,” he added.
The adviser said Mr Biden will “communicate his strong view that the Good Friday Agreement – which is the touchstone of peace and stability in Northern Ireland – must be protected.
“And we must collectively take steps – the US, the UK, the parties in Northern Ireland, the Republic of Ireland – to ensure that it is protected,” he added.
Ms Truss’s official spokesman said on Tuesday that the protocol is an issue “we want to resolve this with the EU” when questioned why she did not discuss it with Mr Macron.
Mr Sullivan welcomed Ms Truss’s “robust and unwavering support for Ukraine’s sovereignty and territorial integrity” and said Russia’s invasion would be a point of conversation.
The “challenges posed by” China, the energy crisis and the “economic relationship between the US and the UK” were also billed.
He accepted Ms Truss’s prediction that a comprehensive US-UK trade deal, which Brexit supporters touted as a major prize of leaving the EU, is years away.
Ms Truss had told reporters: “There aren’t currently any negotiations taking place with the US and I don’t have an expectation that those are going to start in the short to medium term.”
Mr Biden was meant to hold talks with the Prime Minister in the UK as he visited to attend the Queen’s funeral, but they were delayed until Ms Truss’s US trip.