| 1 | Tue 14 Aug 2012 | 90-3 v Yeovil TownYeovil Town 3-0 Colchester United | Capital One Cup First Round |
| 2 | Sat 18 Aug 2012 | 90-0 v Preston North EndPreston North End 0-0 Colchester United | npower League One |
| 3 | Tue 21 Aug 2012 | 92-2 v PortsmouthColchester United 2-2 Portsmouth | npower League One |
| 4 | Sat 25 Aug 2012 | 91-1 v Sheffield UnitedColchester United 1-1 Sheffield United | npower League One |
| 5 | Sat 1 Sep 2012 | 90-4 v Tranmere RoversTranmere Rovers 4-0 Colchester United | npower League One |
| 6 | Sat 8 Sep 2012 | 90-1 v BrentfordBrentford 1-0 Colchester United | npower League One |
| 7 | Sat 15 Sep 2012 | 91-2 v Doncaster RoversColchester United 1-2 Doncaster Rovers | npower League One |
| 8 | Tue 18 Sep 2012 | 91-1 v Crawley TownColchester United 1-1 Crawley Town | npower League One |
| 9 | Sat 22 Sep 2012 | 90-1 v Scunthorpe UnitedScunthorpe United 1-0 Colchester United | npower League One |
| 10 | Tue 2 Oct 2012 | 91-0 v Swindon TownSwindon Town 0-1 Colchester United | npower League One |
| 11 | Sat 3 Nov 2012 | 91-3 v Chelmsford CityChelmsford City 3-1 Colchester United | FA Cup with Budweiser First Round |
| 12 | Tue 6 Nov 2012 | 90-2 v Notts CountyColchester United 0-2 Notts County | npower League One |
| 13 | Sat 10 Nov 2012 | 92-3 v Crewe AlexandraCrewe Alexandra 3-2 Colchester United | npower League One |
| 14 | Sat 17 Nov 2012 | 92-0 v BuryColchester United 2-0 Bury | npower League One |
| 15 | Tue 20 Nov 2012 | 91-3 v Coventry CityColchester United 1-3 Coventry City | npower League One |
| 16 | Sat 24 Nov 2012 | 91-5 v Milton Keynes DonsMilton Keynes Dons 5-1 Colchester United | npower League One |
| 17 | Sat 8 Dec 2012 | 90-2 v Oldham AthleticColchester United 0-2 Oldham Athletic | npower League One |
| 18 | Sat 15 Dec 2012 | 90-1 v BournemouthBournemouth 1-0 Colchester United | npower League One |
| 19 | Sat 22 Dec 2012 | 90-1 v WalsallWalsall 1-0 Colchester United | npower League One |
| 20 | Wed 26 Dec 2012 | 91-3 v BrentfordColchester United 1-3 Brentford | npower League One |
| 21 | Tue 1 Jan 2013 | 90-3 v Crawley TownCrawley Town 3-0 Colchester United | npower League One |
| 22 | Sat 12 Jan 2013 | 91-2 v Scunthorpe UnitedColchester United 1-2 Scunthorpe United | npower League One |
| 23 | Tue 5 Feb 2013 | 90-1 v Swindon TownColchester United 0-1 Swindon Town | npower League One |
| 24 | Sat 23 Feb 2013 | 91-5 v Tranmere RoversColchester United 1-5 Tranmere Rovers | npower League One |
| 25 | Tue 26 Feb 2013 | 92-0 v Yeovil TownColchester United 2-0 Yeovil Town | npower League One |
| 26 | Sat 2 Mar 2013 | 92-0 v StevenageStevenage 0-2 Colchester United | npower League One |
| 27 | Tue 5 Mar 2013 | 90-0 v Hartlepool UnitedHartlepool United 0-0 Colchester United | npower League One |
| 28 | Sat 9 Mar 2013 | 91-2 v Crewe AlexandraColchester United 1-2 Crewe Alexandra | npower League One |
| 29 | Tue 12 Mar 2013 | 92-2 v Coventry CityCoventry City 2-2 Colchester United | npower League One |
| 30 | Sat 16 Mar 2013 | 92-1 v BuryBury 1-2 Colchester United | npower League One |
| 31 | Fri 29 Mar 2013 | 90-1 v BournemouthColchester United 0-1 Bournemouth | npower League One |
| 32 | Mon 1 Apr 2013 | 81-1 v Oldham AthleticOldham Athletic 1-1 Colchester United | npower League One |
| 33 | Sat 6 Apr 2013 | 92-1 v Leyton OrientColchester United 2-1 Leyton Orient | npower League One |
| 34 | Sat 13 Apr 2013 | 91-3 v Notts CountyNotts County 3-1 Colchester United | npower League One |
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