Alliance has 24 Fokker 100s, 13 Fokker 70LRs and 20 Embraer E190 jets in service and will add 13 more E190s to the fleet next year.
Three E190s are currently leased out to a third party.
The fly-in, fly-out air charter company used the Fokker 50s on the Adelaide to Olympic Dam route to ferry BHP workers, however, with the Olympic Dam runway upgraded to accommodate jet aircraft it was deemed more economical to use the bigger Fokker 100 and E190 jets.
After reviewing the use of the old turboprop aircraft, Alliance decided to retire the fleet early and sell it off.
The sale includes the five Fokker 50s, associated spare engines, parts, tooling and ground support equipment.
In a statement to the Australian Securities Exchange Alliance said the sale would result in a non-cash write down of $12.1 million and statutory loss of $7.1 million for 2022.
"This fleet change will result in substantial cost savings related to engineering, crewing, infrastructure and training costs, which the company estimates to be about $4.4 million per annum," the company said.
"The carrying value of the remaining Fokker jet fleet, which is scheduled to continue to operate for at least ten years, is not impacted in anyway by this fleet rationalisation."
Alliance is expected to record profit before tax of $45.3 million in 2022 despite impacts from ongoing COVID-19 restrictions on flight crew and disruption to service providers such as airports, security screening, caterers and ground handlers.