[6] After the conclusion of the 1966–1967 Beta Ethniki season, the club was forcibly relegated to amateur status through a legislation, that allowed each regional city of Greece to be represented in the country's Second national Division by a single team only.

[13] However the most notable feat of this period came during the 1985–86 season, when Ergotelis, at the time playing in the Gamma Ethniki, managed to reach the Greek Cup quarterfinals, which would remain the best performance of the club in the competition for 33 years.

In the late 90s Ergotelis' came under the ownership of veteran football directors Georgios Soultatos and Nikos Tzortzoglou, who took over the club for the third time after two relatively successful tenures during the 90s.

[18] Learning from past experience, careful transfers of promising players from the Cretan market were made, while an emphasis was placed on the development and growth of the club's infrastructure, leading up to the establishment of the Ergotelis Youth Academy at Martinengo Stadium.

[18][19] Within a couple of years, Ergotelis grew into a strong, competitive team composed mostly of Cretan players, that would celebrate three consecutive promotions from the 4th Division to reach the Alpha Ethniki, the highest professional football league in Greece for the first time in club history.

[19] Ogunsoto personally scored 30 goals in 32 games, with emblematic team captain Stavros Labrakis adding in another 12, both significantly contributing to the club's triumphant return to the Beta Ethniki after a 31-year absence.

[19] In the following season, Ergotelis participated in the Beta Ethniki, once again leveraging on a string of strong home game performances (eleven wins, three draws and only one loss), backed by a fierce support of the club's fans.

On May 30, 2004, Ergotelis won that match, defeating Athenian club Akratitos 1−0 at the neutral Makedonikos Stadium in Thessaloniki in front of a cheering crowd of 2,000 fans travelling from various corners of the country, thanks to an injury time goal by Jean Marie Sylla.

On the sidelines, the club took full advantage of the new stadium during its debut season in the Alpha Ethniki, attracting fans from all over Crete and earning recognition by both the Greek state and Hellenic Football Federation.

[22] The following year however, after overcoming a rough start to the 2005–06 season, Ergotelis returned to good form after Greek manager Nikos Karageorgiou took over in mid-season, achieving instant promotion back to top-flight and winning its first-ever Beta Ethniki title.

During Papoutsakis' presidency, the club rose to prestigious standards in Greek football, which eventually earned Ergotelis consecutive Fair Play awards, for the 2008–09[25] and 2009–10 seasons.

Coping with the change in leadership, Ergotelis finished a turbulent 2007–08 season, barely avoiding relegation on the final match day thanks to a combination of league results, which allowed the club to capitalize on its 2–0 home win vs. Xanthi in front of 10,000 cheering fans.

[29] Moreover, Ergotelis organized a series of social and beneficial activities, and fittingly commemorated its anniversary with a stunning 5–0 thrashing of reigning champions Olympiacos in a friendly game held at Pankritio Stadium on September 6, 2009.

[31] Outside the pitch, the club's board of directors would gain praise from the media for its initiative to sign international partnerships with Dutch side FC Utrecht[32] and State-side Philadelphia Union.

While the season took off on a promising start, subsequent weak performances, along with rising tensions between several of the club's players and the manager, ultimately failed to keep Ergotelis in top-flight.

The team was relegated in the end of the season, after a disastrous second round which saw the club win only 2 of the total 15 matches, and thus return to the 2nd tier (which had been renamed as the Football League) after finishing in 14th place.

[48] The club hired Bosnian manager Jasminko Velić and began preparations for the Football League almost a month after the season was officially declared started.

The latter's officials decided that the Football Club should thus be dissolved and enter into liquidation, a process that would allow Ergotelis to compete in amateur competitions under new leadership, free of the financial obligations of the previous administration.

As the club brought in former Ergotelis stars such as Sergio Leal and Nikolaos Katsikokeris to lead the effort on the pitch and filled the roster with veteran Football League players, the new administration's project eventually paid off.

[61] For the first season in the Football League under Samy's presidency, Ergotelis boasted a youthful team led by controversial Greek manager Takis Gonias.

They went on to eliminate local Super League rival OFI in the knock-out phase to eventually make it to the quarter-finals for the first time since 1986, matching the club's best-ever performance in the competition.

However, they were eventually deducted three points for failing the economic oversight process requirements of the HFF,[63] and thus finished in 4th place, securing its participation in the newly established Super League 2.

[64] In a season that was cut short due to the COVID-19 pandemic,[65] Ergotelis failed to repeat their previous year's performance, eventually finishing in seventh place with 29 points.

This decision was approved by the Hellenic Football Federation (EPO), and the club became the 17th team to participate in the league, prompting the local association to hold a new draw.

Ergotelis first logo survives from the historical document of the club's establishment, and depicts a runner surrounded by a laurel wreath, similar to the ones awarded to the ancient Olympic Games victors.

Early photographs of Ergotelis' football department and fans depict an alternate club logo, simply the letter E possibly framed within a circle.

[70] In 2009, the club issued an anniversary logo, which used a slightly darker palette and featured a smaller version of the laurel wreath and athlete, framed within a golden 80, part of the phrase "80 ΧΡΟΝΙΑ 1929–2009" (English: "80 YEARS 1929–2009").

During its first season in the competition, Ergotelis averaged almost 10,000 supporters during home games, and consequently set the Pankritio Stadium's attendance record on 20 February 2005, in a 2−1 Super League victory over reigning champions Olympiacos with 27,950 tickets being sold-out.

Ergotelis' side claimed their relegation to be retaliation for allowing renowned left-liberal songwriter and composer Mikis Theodorakis to perform a concert in Martinengo Stadium, giving political dimensions to the already strained relations between the two clubs.

Ergotelis on the other hand, loaned their longtime scoring legend Patrick Ogunsoto to a financially weakened Beta Ethniki side OFI in 2010 for no fee, as an attempt to assist their prestigious rival in their struggle to once again return to the Super League.