Aside from cargoes, the Port also serves as a major hub for seafaring passengers going to major destinations in Visayas and Luzon islands. It is part of the Central Nautical Highway under the Roll-On Roll-Off Transport System linking Mindanao to Cebu, Iloilo, Bacolod, Jagna and Tagbilaran cities in Visayas, and Manila and Batangas in Luzon.

The two-storey Passenger Terminal Building (PTB) in the Port of Cagayan de Oro can cater up to 3,000 passengers at any given time. Additionally, it is equipped with facilities for maximum safety, security, comfort and convenience of the passengers, that include: Security Checkpoint 2 with X-Ray scanner for luggage/baggage, body scanner, CCTVs; Security Office; Collector’s Booth; Public Assistance and “Malasakit” Desk; and Offices for passenger-related agencies such as Quarantine, Tourist Police and Coast Guard. It also houses GAD amenities such as Play Area for children; Child Care Station for breastfeeding and diaper changing; Ecumenical Prayer Rooms, medical clinic, separate toilet facilities for PWDs (Female and Male) among others. The PTB is also powered by high-speed internet wifi connection and has free charging stations.

Porterage service is being provided by the Macajalar Wharf Porters Association.