The climatic differences between Greece and Egypt made it possible to excavate in both countries each year and late in 1928 Pendlebury started excavating at Tell el-Amarna, in Egypt. In 1929 he was fortunate to be appointed by Arthur Evans curator of the archaeological site at Knossos in central Crete. Doubly fortunate the job came with the Taverna, situated on the edge of the site this house provided accommodation for married couple and a centre for social activities amongst the archaeologists.
Pendlebury was one of the early archaeologists who engaged in environmental reconstruction of the Bronze Age; for example, as C.Michael Hogan notes, Pendlebury first deduced that the settlement at Knossos on Crete appears to have been overpopulated at its Bronze Age peak based upon deforestation practises.
Pendlebury was Director of Excavations at Tell el-Amarna from 1930 to 1936 and continued as Curator at Knossos until 1934. From 1936 he directed excavations on Mount Dikti in eastern Crete and continued there until the war was imminent.
Patrick Leigh Fermor said:
... [Pendlebury] got to know the island inside out. ... He spent days above the clouds and walked over 1,000 miles in a single archaeological season. His companions were shepherds and mountain villagers. He knew all their dialects...".Manolaki Akoumianos, a Cretan and one of the workers at Knossos, said:
...[he] knew the whole island like his own hand, spoke Greek like a true Cretan, could make up mantinadas all night long, and could drink any Cretan under the table.
Anticipating the coming war and strategic nature of Crete, Pendlebury eventually succeeded in convincing the British military authorities of the value of his unique knowledge. They sent him back to England for military training, and in May 1940 he returned to Heraklion (then called by its Italian/Venetian name - Candia) as British Vice Consul, but his job title did not hide from most of the diplomatic community the nature of his duties. He immediately set-to working up his outline plans: improving the reconnaissance (routes, hiding places, water sources and chiefly sounding out the local clan chiefs like Antonios Gregorakis and Manoli Bandouvas. Turkey had relinquished control over Crete only 43 years before and these kapetanios would be the key to harnessing the Cretan fighting spirit. In October, on Italy's attempted invasion of Greece, Pendlebury became liaison officer between British troops and Cretan military authority.
By the time Germany had successfully occupied mainland Greece in April 1941 Pendlebury had laid his plans, unfortunately they could not include the Cretan division of the Greek army which was captured in Greece. The invasion of Crete started on 20 May 1941, Pendlebury was in the Heraklion area where it started with heavy bombing followed by troops dropped by parachute. The enemy forced an entry into Heraklion but were driven out by regular Greek and British troops and by islanders now armed with assorted weapons.
On 21 May 1941, when German troops took over Heraklion, Pendlebury slipped away with his Cretan friends heading for Krousonas the village of Kapetanios Satanas, which was some 15km to the southwest. They had the intention of launching a counter attack, but on the way there Pendlebury left the vehicle to open fire on some German troops, who fired back. Some Stukas came over and Pendlebury was shot in the chest. Aristeia Drossoulakis took him into her nearby cottage and he was laid on a bed. The cottage was overrun and a German doctor treated him chivalrously, dressing his wounds; he was later given an injection.
The next day Pendlebury had been changed into a clean shirt. The German were setting up a gun position nearby and a fresh party of paratroopers came by. They found Pendlebury who had lost his identity discs and was wearing a Greek shirt. As he was out of uniform and could not prove that he was a soldier, he was put against a wall outside the cottage and shot through the head and the body.
He was buried nearby, later being reburied 1km outside the western gate of Heraklion. He now lies in the cemetery (Grave reference 10.E.13) at Souda Bay maintained by the Commonwealth War Graves Commission.