In a 1997 article from the Journal of Air Transportation, Mesa's safety record was noted as having the fewest incidents among domestic regional airlines at that time.

In 1981 as the original Frontier Airlines (1950-1986) was discontinuing its flights between the two cities, Mesa obtained a twin-engine Piper Navajo Chieftain and increased service on the route.

The Risleys quickly expanded the carrier by acquiring a fleet of 14-passenger seat Beechcraft Model 99 commuter turboprops and adding service throughout New Mexico and surrounding states with a hub at Albuquerque.

These routes were originally from the independent Mesa operation and Several Beechcraft 1900D aircraft were painted in the America West Airlines scheme.

In 1995, Mesa created a new subdivision called Desert Sun Airlines and acquired a pair of Fokker 70 jets for use on new America West Express routes from Phoenix to Des Moines and Spokane.

Beginning in December 1997, Mesa began operating Dash 8-200 aircraft between Phoenix and Grand Junction followed by many other cities throughout Colorado, New Mexico, Arizona, and California.

As Mesa began taking deliveries of the Embraer ERJ 145 aircraft in 2000, the CRJs were transferred to the America West division, separating the fleet types.

US Airways Express routes from Charlotte and Phoenix were gradually shifted to American Eagle until the transition and merger was completed on October 17, 2015.

Midwest Express kept the Skyway Airlines name and routes, forming Astral Airways to fill the void as Mesa ceased service in Milwaukee.

America West Airlines closed its Columbus hub in 2003 and Mesa again reallocated the assets this time to its newly reacquired United Express operation.

[citation needed] Mesa created CalPac (California Pacific) in 1992, establishing a second United Express carrier with a Los Angeles hub along with WestAir.

[citation needed] The Desert Sun Airlines division was created in 1995 to inaugurate Mesa's first jet service utilizing Fokker 70 aircraft.

There was also a previous Desert Sun Airlines not affiliated with Mesa that operated scheduled passenger commuter service in southern California during the mid-1980s with Beechcraft 99 turboprops and Piper Chieftain prop aircraft.

It established a code share with Mokulele Airlines, which served airports that cannot accept jet aircraft and provide point-to-point service in between the islands with Cessna Caravan turboprops.

Air traffic controllers were unable to reach the two pilots for 25 minutes, after which contact was re-established and the aircraft returned for a safe landing in Hilo.

In response Mesa Airlines CEO Jonathan Ornstein stated "We're going to continue to negotiate on good faith and come to an agreement that the company can afford" and that it "takes reasonableness on both parties.

While the strike vote had the intended effect, the company still offered a negligible[clarification needed] pay increase that would keep flight attendants to what they have calculated as "Industry Average".

On April 25, 2017, members of the AFA who were not employees of Mesa carried out informational protests in Chicago, Dallas, and Phoenix to educate the public about the union's concerns such as low wages, poor health insurance, lack of progress on contract negotiations, as well as other actions of the company, and gain attention from American and United.

[32] The union stated "it soon became apparent the Company was not prepared to reach a deal and saw no point in bargaining until after they knew the outcome of the pilots' vote which will be counted on July 12."

The AFA and Mesa Airlines reached a Tentative Agreement on August 14 and included these changes: On March 2, 2017, the Air Line Pilots Association, International union representing all of Mesa Airlines pilots filed a lawsuit after wages had stagnated and ceased to increase in any amount for almost ten years and the company had allegedly bypassed the Railway Labor Act by implementing bonus and incentive programs without reaching an agreement beforehand with the ALPA.

[33] The goal of the pilots is similar to the at-the-time objective of the flight attendants, which is to be paid a standard and comparable wage to other regional airlines that can substantiate necessities such as food and shelter.

The incident was not reported by either pilot to the company and the airplane was allowed to be flown by the next crew the following morning on its scheduled service back to Charlotte, North Carolina, where a post flight inspection revealed the tail strike.

When interviewed, the captain first denied having been involved in a hard landing and speculated that the tail strike must have been the result of an over rotation on takeoff from the morning crew.

She reported that she briefed "no go-around" because no takeoffs were authorized on the runway at night or in IMC conditions; however, the first officer knew this was incorrect, but did not challenge the captain.

It is remarkable that the damage to the tail section was not discovered during the preflight visual inspection performed by the morning flight or ground crews.

Bombardier CRJ200 fell asleep and overshot their destination airport by 26 nautical miles (48 km; 30 mi) before air traffic control was able to make contact with the aircraft.

The National Transportation Safety Board determined the probable cause of this incident as follows: "The captain and first officer inadvertently falling asleep during the cruise phase of flight.

Contributing to the incident were the captain's undiagnosed obstructive sleep apnea and the flight crew's recent work schedules, which included several consecutive days of early-morning start times.

[40] On January 11, 2019, American Eagle Flight 5766, en route from Dallas-Fort Worth, slid off the runway after landing in icy and snowy conditions.

The Bombardier CRJ900 was the first flight to attempt to land at Columbia Municipal Airport after the ground crew cleared the runway of ice and snow.