[7] In the same year, Panagiotis Stamatakis, the Ephor General in charge of the Greek Archaeological Service, invited Tsountas to accompany him on a tour of Boeotia, combatting the illicit trade in antiquities — an event which has been described by the archaeological historian Eleni Konstantinidi-Syvridi as the beginning of Tsountas's apprenticeship to Stamatakis.

After the hiring of Panagiotis Kavvadias in 1879 and of Konstantinos Dimitriadis in 1881, Tsountas was recruited by Stamatakis as an ephor alongside Demetrios Philios; they would be joined by Valerios Stais, Vasileios Leonardos and Georgios Lampakis in 1885.

[27] In the same year, he excavated on the western slope of the citadel, in the area of a Hellenistic tower, and uncovered a building complex later identified as part of the site's "Cult Centre".

[21] In 1888, Tsountas made further excavations of the palace, as well as in the eastern part of the citadel, particularly the North East Extension and Mycenae's subterranean cistern,[28] which he discovered.

[13] Excavations here continued in 1889, during which time Tsountas made further explorations of the south-western part of the citadel, uncovering a series of buildings over several seasons of work but making little record of them.

[32] In contrast to the orthodoxy then prevalent, Tsountas considered the chamber tombs and tholoi at the site to postdate the shaft graves of Circle A.

[35] The region of Thessaly, in northern Greece, had been the subject of brief and informal antiquarian investigations in the final decades of Ottoman rule prior to 1881.

The region was incorporated into the Greek state in 1881, and therefore came under the jurisdiction of the Greek Archaeological Service; this development intensified efforts to collect and conserve known antiquities, still largely on an informal basis – the headteachers of local gymnasia would often be designated by the Archaeological Service as "Occasional Collectors of Antiquities" and organise small collections of portable finds, sometimes working alongside foreign scholars such as the German archaeologist Habbo Gerhard Lolling.

[3] In the course of excavating five Mycenaean tombs at the site,[39] he uncovered levels of settlement deposits dating to the Neolithic period, providing the first evidence of Neolithic material in Greece and demonstrating that mounds of this kinds, known as magoules, could be tells formed from the deposited layers of settlements of successive periods.

[45] In September 1894, he excavated the cemetery of Amorgos, an island already known for its quantity of prehistoric remains, including graves dating to the Early and Middle Bronze Age.

[46] He was guided by a local priest, Dimitrios Prasinos, who had previously directed other archaeological visitors to the island and sold low-value antiquities to foreign archaeologists, including Duncan Mackenzie.

[55] Tsountas excavated frequently on the island of Euboea, which he considered an important influence on the Cycladic Syros culture.

[60] He was assisted by Stefanos Xanthoudidis [el], the Ephor of Antiquities for Crete; Iosif Chatzidakis [de], the founder of the Heraklion Archaeological Museum; Arthur Evans, the archaeologist of the Minoan palace of Knossos; and Harriet Boyd, who had discovered and excavated the site of Gournia.

[66] The school's thirty-six students in its first year included Karouzos, Semni Papaspyridi and Spyridon Marinatos, all of whom went on to become leading figures in twentieth-century Greek archaeology.

[68] Encouraged by Arthur Evans, Tsountas granted permission for the British archaeologist Alan Wace to excavate at Mycenae in the early 1920s.

[50] The place of his burial is unknown: the historian Eleni Manteli has suggested that the Greek state likely neglected to organise a funeral or memorial for him.

[73] Tsountas believed that Greek culture had existed in a continuous form since the prehistoric period, developing the ideas of historians such as Constantine Paparrigopoulos,[65] who had sought in the mid-nineteenth century to challenge the then-popular view that the population of modern Greece had no biological or cultural descent from that of the classical period.

[76] Tsountas argued that the Mycenaeans had originally been immigrants from northern Europe, with genetic commonalities with the Germans, Celts and Italians.

[77] Like other archaeologists and folklorists of his day, such as the German Arthur Milchhöfer and the French Georges Perrot, Tsountas assessed the cultural continuity of Greece through perceived similarities in vernacular customs and architecture; he drew attention, for example, to the similar shape of hearths found in Mycenaean dwellings and modern Greek peasant homes.

[82] In an obituary of Tsountas published in the newspaper Nea Estia, his former student Karouzos described him as an "excellent teacher ... [and] modest man" with a "Socratic" appearance.

[85] Tsountas has been considered an underappreciated figure in Aegean archaeology, particularly by comparison to non-Greek archaeologists such as Schliemann, Wace and Evans.

[87] According to the historian Cathy Gere, Tsountas is "the individual who properly deserves the title of Father of the Greek Bronze Age".

[22] His excavations in Thessaly have been credited by the archaeologist Curtis Runnels as the beginning of the systematic investigation of the Greek Stone Age.

[89] Tsountas popularised the term Mycenaean to refer to the civilisation of the Greek mainland in the Late Bronze Age.

[1] He is credited with establishing Thessaly as the primary locus of research into Neolithic Greece,[50] while his work in the Cyclades has been recognised with beginning the study of the prehistoric period in those islands.

[18] Tsountas's views of Mycenaean civilisation as fundamentally Greek were initially at odds with the prevailing opinion in scholarship outside Greece, which variously saw the burials in Grave Circle A – before Tsountas's work, considered the totality of evidence for Mycenaean civilisation – as belonging to Near Eastern, Egyptian, Slavic or northern-European cultures.

[34] In most cases, he retained only finds of metal and of stone, as well as intact vases – which were extremely rare – and discarded the remainder.

[93] Since Tsountas's excavations, studies of the spoil created by them has revealed important potsherds, representing substantial fragments of vessels as well as evidence for the later occupation of Mycenae after the end of the Bronze Age.

[95] His assertion that Mycenaean society was illiterate was overturned by the discovery of Linear B tablets at Pylos in 1939, and subsequently, under Alan Wace, at Mycenae in 1952.