On first glance, Cork City looked to have begun the 2006 campaign wearing the new striped shirts that were premiered in the previous year's FAI Cup final loss to Drogheda United. On second glance, however, one notices a small change, with the collar insert now red rather than white. These modified shirts were worn without the eircom League logo in the opening Setanta Cup game against Portadown (far left, only in long sleeves), before the patches were added for the start of the league (left).

Despite the league win, the squad was weakened with the departures of Liam Kearney and Greg O'Halloran to Shelbourne, and John O'Flynn left again for cross-channel football only to return on the eve of the season. The defence
of the title began with a 1-0 win against Dublin City (though a lot of the fans who had been there for the '05 title decider were strangely absent on this occasion), and that paved the way for a solid, if unspectacular, start, with the first three home games won and the first three away drawn. The third of those, away to Bray Wanderers, saw City in the 'Capital of Culture' shirt, which had been promoted to the away choice (right), though the league crests were only on the right sleeves.

Another change came in the 2-0 win at home to Sligo Rovers at the start of May. The visitors turned up Turner's Cross in their away strip of white shirts and red shorts, so to help alleviate the clash City wore the green shorts from the away kit of the previous season (left)
While a first league defeat was suffered away to St Patrick's Athletic, things got back on track with a come-from-behind 2-1 victory over Shelbourne at the Cross on May 15 left them just a point behind leaders Derry City, albeit with two more games played. The next game was away to Derry at the Brandywell, but unfortunately it would be a 2-0 loss, and a 4-0 win away to Dublin City  would be annulled after that club would be forced to withdraw from the league. A 0-0 draw away to Bohemians was unremarkable except for George O'Callaghan's sending-off and that would have repercussions as he and manager Damien Richardson had a falling-out which would result in him not playing and ultimately leaving the club. Despite O'Callaghan's absence, City would overcome Apollon Limassol in the qualifying round of the Champions League, wearing the usual altered kits with just one sponsor and big shorts numbers (home left and away right).
The next round pitted City against Red Star Belgrade, and O'Callaghan would feature - but it would be new centre-back Brian rather than George as a 1-0 defeat was suffered at home before a 3-0 defeat away, a game which saw City wear green shorts and socks (left) to avoid a clash with the white of the home side. While a 1-0 win over Drogheda at the end of June had put City briefly back on top of the table, on their return to league action after the exit from Europe they found themselves having to play catch-up, lagging behind in what had become a four-way battle for the title between themselves, Shels, Drogheda United and Derry. The FAI Cup interest had ended with a controversial loss to Longford Town (which Richardson was none too happy about) but City had a great chance to strike a decisive blow in the league with the trip to Tolka Park to face Shels on August 12, but while Denis Behan and Roy O'Donovan twice put them ahead, a late Glen Crowe equaliser saved Shels, keeping them and Derry eight clear of City on 38 points, with Drogheda on 32.
A week later, Derry's trip south resulted in another 1-1 draw, and then City made three draws in a row against fellow title challengers as a scoreless draw was played out in United Park against Drogheda, leaving them 11 behind Shels, with hopes of a two-in-a-row rapidly fading. As was traditional by now, the 'European' shorts with the larger numbers were called into action for league games (home left and away right and above right), and while the run of draws was ended with a win at home to Bohs, games against UCD and Longford also finished level and while a re-arranged game at home to Bray Wanderers finished 6-0 as Roy O'Donovan scored a hat-trick, the following week the Seagulls triumphed 2-1 against City at the Carlisle Ground.
Nevertheless, hope was never lost and a run of wins against Sligo, St Pat's and Waterford, coupled with Shels and Derry dropping points, left City just six points behind Shels and level with Derry, with Drogheda just a point behind, ahead of the penultimate round of games. The fixtures computer had Shels coming to the Cross for the second-last game, while the final round again saw a City-Derry clash, albeit this time at the Brandywell. City managed to achieve the first part of what was still a mammoth task, Neale Fenn's goal securing a 1-0 win against Shels, but the Dublin side's superior goal difference meant a nine-goal swing was required, and as Shels were playing ninth-placed Bohemians, it was unlikely. In any case, City lost 1-0 away to Derry, pairing green socks with white shorts (right), meaning they had worn all four combinations of shorts and socks during the season. Shels won 2-1 to take the title on goal difference and Drogheda's win over Waterford relegated City to fourth place. It was not a disaster, but there was a feeling that it would not have taken too much more to repeat the 2005 heroics.