Air Malta aims to provide the quality service to passengers, providing hot and healthy meals for Business Class passengers. Passengers with special dietary needs are able to pre-order their meal at least 48 hours before their scheduled flight. Air Malta also offers a wide selection of products through their unique Sky Bar Menu for Economy Class passengers, which passengers can purchase food and drink items from. This service is not available on some of Air Malta's shorter routes.

The mileage and frequent flyer program for Air Malta is called Flypass, letting passengers earn and use points called KMiles to purchase tickets or flight upgrades. Air Malta is not part of an airline alliance however the airline is partnered with Lufthansa and Swiss Air allowing passengers to earn and use miles between each airline.

Air Malta lets Economy Class passengers check in at airport counters until 45 minutes before the scheduled departure time for flights. Business Class passengers with hand luggage only can usually check it up to 30 minutes before departure time. Online check-in for Air Malta is available 24 hours before the departure time and closes two hours before.