Following the German occupation in June 1941, the airbase was reconstructed, and a squadron of reconnaissance aircraft was established, using forced labour from the local population.

[9] On 4th July 1943, a British Special Air Service (SAS) raiding party led by Danish military officer Anders Lassen attacked Kastelli Airfield to divert German attention during the Allies' preparations for the invasion of Sicily.

The raiders marched over sixty miles across Crete, successfully placing explosives on multiple aircraft before retreating under heavy fire.

In 2016, the Greek government officially tendered the construction of a relocated Heraklion airport adjacent to Kastelli Air Force Base to address the capacity and expansion issues.

The existing airport at Heraklion will be closed and an area of 278 ha (690 acres) there will be returned to local communities for a large urban regeneration plan.

The creation of the new airport will require new road, water and sanitation works, as well as the transfer of settlements located within the proposed runway zone (Archangelos, Roussochoria).

[18] Initially,[19][20] four candidates had appeared for the Kasteli airport construction and management project, from Greece, China, France and Spain.

According to the Greek Secretary General of the Ministry of Infrastructure and Transport, Mr. Giorgos Dedes, €10 million have been approved for expropriations and the contract for the airport has been approved by the Court of Auditors, so that infrastructure works can begin in January 2019, even if there are great concerns about the environmental pollution from airplane fumes to the underground water deposits that provide water to 1/4 of the city of Heraklion.

[24] The construction phase of the airport commenced in February 2020 after Greek Prime Minister Kyriakos Mitsotakis laid the foundation stone.

[27] In June 2024, construction crew discovered an ancient Minoan architectural ensemble on the top of Papoura Hill where a radar system was planned to be built.

After meeting with Greece’s Culture Ministry, planners decided to prioritize the excavation and protection of the ancient structure while concurrently continuing airport construction in other areas.