Its hub, operations and maintenance base was Juan Santamaría International Airport (SJO) having moved in 2013 from its original location at Aeropuerto Internacional Tobías Bolaños (SYQ).

[5] On 31 December 2017, all 10 passengers and two pilots aboard Nature Air Flight 144 were killed in an aerodynamic stall shortly after takeoff from Punta Islita airstrip.

Although the accident was ultimately determined by the NTSB to have been caused by pilot error, Nature Air stopped flying in January 2018 and its operating license was indefinitely suspended by the civil aviation authority of Costa Rica on May 2, 2018 leading to the closure of the airline.

[7][8] Between 2001 and 2016, the airline grew under its new management team and brand, boosted by the increasing popularity of Costa Rica as an eco-tourism and adventure travel destination.

[9] The airline calculated the tons of carbon released from the fuel burned each year in flight and ground operations and donated a corresponding amount of money to FONAFIFO, a rainforest financing division of the Environment Ministry.

In November 2011, Nature Air introduced two Cessna 208 Grand Caravan aircraft to its fleet for the first time, configured for 12 passengers and 2 pilots.

[13] The airline established the NatureKids Foundation, a non-profit entity that provided English language and basic computer education to young children living in the Drake Bay district of the Osa Peninsula of Costa Rica.