The Conference National ended in chaos in 2005-06.

Firstly, Canvey Island resigned, following the resignation of their main financial backer, at the end of the season and dropped three divisions. This reprieved Tamworth from relegation.

Then, Altrincham were deducted 18 points after playing James Robinson, whose previous club, Accrington Stanley, had failed to get international clearance for him. Despite the FA issuing a letter to Altrincham confirming no breach of FA or FIFA rules, the Conference deducted the 18 points and fined Altrincham £1,000.

Shortly after fining Accrington a mere £200 for the offence, the FA upheld the Conference's decision regarding Altrincham.

At the Conference AGM in Birmingham on 3 June 2006, Scarborough were demoted for allegedly breaching Conference rules relating to their financial arrangements, thereby reprieving Altrincham.

Meanwhile, Crawley Town lost just three points for breaching the wage cap and other financial irregularities. Crawley announced that they would go into administration during the close season and, if so, would start 2006-07 with a ten-point deduction.

At the top of the table, Hereford won the play-off final against Halifax Town to joined Accrington Stanley in League Two.

Below is the table showing the close-season deductions, followed by the table as it was beforehand.