The Ecolog era

During the 2012–13 season, Shkëndija was embroiled in financial difficulties and as a result, many of its players left the club earlier in the summer. The Shkëndija supporters, the Ballistët, began a social media campaign requesting Ecolog to take over Shkëndija.<sup class="reference" id="cite_ref-A_6-0">[6]</sup> Albanian international, Lorik Cana and Swiss international, Xherdan Shaqiri also joined the campaign with the supporters.<sup class="reference" id="cite_ref-A_6-1">[6]</sup> On 31 July 2013, Lazim Destani, father of Ecolog founder and chairman, Nazif Destani, announced Ecolog International will take charge of Shkëndija.<sup class="reference" id="cite_ref-A_6-2">[6]</sup><sup class="reference" id="cite_ref-b_7-0">[7]</sup> Under the new administration, Shkëndija bought in over five new players to the squad, four days before the transfer season ended, as well as balancing the financial state of the club. The new season started averagely for Shkëndija, amassing five draws in a row. However, on 21 September 2013, Shkëndija comfortably defeated rivals FK Vardar in a 3–1 home game during the derby, displaying improvement of the club under Ecolog. However, for the next eight fixtures, Shkëndija were very inconsistent, drawing once, winning three and losing four. After losing 5–0 to FK Rabotnički, manager Gjore Jovanovski was relieved of his duties. Shpëtim Duro was named the manager Shkëndija just 15 hours after the sacking of Jovanovski. He was first hired as a temporary caretaker manager for the club's the remaining 3 games before the long winter break, but signed a contract with the club to be the manager for the remainder of the 2013–14 season.<sup class="reference" id="cite_ref-8">[8]</sup><sup class="reference" id="cite_ref-9">[9]</sup>
During the winter break, Shkëndija was the most active team in the Prva Liga during the transfer period, bringing in 9 new players, further revamping the football club in preparation for the second half of the season. The second half of the season saw drastic improvement for Shkëndija under Shpëtim Duro, moving them from 8th position near the relegation zone, to 4th position at the end of the season, winning their final seven games in a row.<sup class="reference" id="cite_ref-10">[10]</sup> Shkendija earned a spot in the 2014–15 first qualifying round of the UEFA Europa League.