In the 8 years to come, and until 2006, the club briefly joined forces with fellow local team Panchaniakos, but ended up losing its quality players to the Nea Chora club and themselves relegated to the local B Division.

Their decline was ongoing, as AO Chania was demoted to the C Division (lowest regional competition level), even finishing in last place during its tenure there, while in 2004 the club was on the brink of a permanent shutdown and dissolution.

Since then, thanks to a salvation movement led by Chania businessmen, the club began a steady rise to restore its former glory.

The club's return to the competition was surpassed by its 2nd-place finish during the Southern Group 2013–14 regular season campaign.

After the latter was forced to relegation to the Gamma Ethniki by the Hellenic Football Federation for failing to renew its league participation certificate, Kissamikos owner at the time Antonis Rokakis proposed a merger of the two clubs in an attempt to form a new, strong outfit to represent the region, and more specifically the city of Chania (as the region's competitor in the Greek Superleague, Platanias is based in the neighboring town and municipality of Platanias).