Air Juan is also the only airline company that offers flights to and from Manila outside the heavily congested Ninoy Aquino International Airport as all its seaplane flights arrive and depart from the Air Juan Seaplane Terminal located within the Cultural Center of the Philippines Complex in Pasay, Metro Manila. Aside from its seaplane operations, the company also has in its fleet helicopters, business jets, and propeller planes for commuter air services in Palawan, Caticlan, and Iloilo.

Air Juan started operating private charter services in 2012, and scheduled flight services from Puerto Princesa to Cuyo Island, Coron, and Caticlan in 2016. Most recently, Air Juan started operating scheduled seaplane services from Manila to Puerto Galera, Subic, Busuanga Bay, and Boracay without passing through domestic airports as the aircraft flies its passengers directly to the hotels or resorts.

In 2017, Air Juan announced that it is expanding its seaplane operations and will soon offer flights from Manila to Marinduque, Baler, and Balesin Island resort, though it is uncertain whether it will be a regular scheduled flight or just through charters. Its Palawan operations have expanded to include Iloilo and Caticlan services from Cuyo Island. In June 2017, Air Juan started operating land planes out of Mactan-Cebu International Airport offering services to Tagbilaran City of Bohol, Siquijor, Biliran, Maasin, Sipalay, and Bantayan Island. In March 2018, Air Juan began commercial flights between Cebu City and Catbalogan City, Samar's capital.

According to worldkings.org