The new president faced mass protests and global outrage over the controversial bar on travellers from Iraq, Syria, Iran, Libya, Somalia, Sudan and Yemen, as around 300 people were stopped or detained worldwide en route to the US.
"We have made the necessary adjustments to our crewing, to comply with the latest requirements," a statement from Emirates said.
The carrier added that no staff member had yet been affected by the travel restrictions and stressed that all flights to the US were operating as scheduled.
Trump signed an executive order on Friday to suspend refugee arrivals for at least 120 days, and to bar visas for three months for travellers from Iraq, Iran, Libya, Somalia, Syria, Yemen and Sudan. The move was met with widespread protests across the country.
The immigration order, however, hit a roadblock when a federal judge issued an emergency order temporarily barring authorities from deporting refugees and other visa holders who have been detained.