In 1980 Fajardo airport was built and Vieques Air Link started flights to the new airport immediately. In the 1980s the company increased the frequency of flights to San Juan, Humacao and Culebra. In 1989, Vieques Air Link lost its entire fleet to Hurricane Hugo. However, it soon acquired seven Britten-NormanIslanders and three Trislanders.
In the 1990s VAL got into financial trouble. With the Vieques conflict, more and more Puerto Ricans began flying Vieques Air Link every day to go to military camps to protest, and the police also had to fly their personnel and the people arrested in those areas on VAL planes at various times. Others, like political leaders Ruben Berrios and Fernando Martín, and the 2002 Miss Puerto RicoCarla Tricoli, who is a Viequense, have had pictures taken by the press aboard VAL planes while flying to Vieques, giving the airline a new wave of unpaid-for promotional attention. In addition, in June 2000, the airline made the cover of Islander News magazine, under the headline "Vieques Air Link: How To Survive a Hurricane", about the airline's fleet loss of 1989 and how it survived the potentially fatal financial disaster.
December 21, 1971 – an Islander, N589JA, with 1 crew and 7 passengers crashed at Culebra airport. Upon landing, The aircraft bounced on landing. The pilot initiated a go-around over hills. The aircraft was unable to clear a house and crashed.
December 19, 1977 – an Islander, N862JA, crashed en route from St. Croix to Vieques when both engines flamed out due to fuel exhaustion. The aircraft was ditched off Vieques. There were 9 passengers and a pilot on board. Five were killed and the aircraft was written off.
On January 26, 1980, a bomb was found on a Vieques Air Link plane that was about to be flown by Raul Mari Pesquera, son of Juan Mari Bras (in Spanish).
August 2, 1984 – an Islander, N589SA, operating as Vieques Air Link Flight 901A, crashed on initial climb out of Vieques en route to St. Croix. The Islander was overloaded by 600–700 pounds when it departed Vieques. Also, its centre of gravity was up to 5 inches behind the aft limit. After takeoff the left engine lost power. It lost altitude, banked abruptly to the left, nosed down and crashed into the ocean. It appeared that the fuel had been contaminated with water. On board were the pilot and 8 passengers, all were killed. 
September 21, 1989 – the following Islanders were damaged beyond repair by Hurricane Hugo.
On May 6, 2000, a Vieques Air Link pilot allegedly flew a company aircraft over Camp Garcia, a restricted US Navy area, on a scheduled flight an hour after protesters had been removed from the area by FBI agents and U.S. Marshalls, resulting in the suspension of the pilot.