Apart from a few sections which came into force on Royal Assent on 8th November 2006, the main Act comes into force on a day or days to be appointed by the Secretary of State (see Armed Forces Act 2006 s.383). The Armed Forces Act 2006 (Commencement No. 1) Order 2007, SI 2007/1442 brought into force on 4th June 2007 the important changes noted below which replace the one-off courts martial that must currently be convened for each trial. Further sections are brought into force on 15th October 2007 and 1st January 2008 by the Armed Forces Act 2006 (Commencement No. 2) Order 2007, SI 2007/2913.

Amongst other changes (as from the date on which the relevant provisions come fully into force - not yet known as at October 2007) the Act wholly repeals and replaces the Army Act 1955, the Air Force Act 1955 and the Naval Discipline Act 1957. These Acts, commonly known as the Service Discipline Acts, provide for the current Courts Martial system under which servicemen and women are tried for disciplinary offences and criminal offence committed anywhere in the world. There is no change to the overriding provision that the main provisions have to be renewed every five years (see s. 382(3) of the Act which, under s.383, came into effect on the passing of the Act ) which derives from that fact that raising a standing army without Parliamentary consent has been illegal since the time of the 1668 Bill of Rights (see notes at Specific employments/army, navy and air force/discipline acts ).

Under the current system each of the three services convenes its own Courts Martial for each trial as and when required and there are many details in which Courts Martial of one service differ from the Courts Martial of the other two services. However there is some "jointery" already in that all have a civilian judge advocate plus not less than three service members and in all cases there is a right of appeal to the Courts-Martial Appeal Court, with civilian judges from the Court of Appeal.

One of the most important purposes of the Armed Forces Act 2006 is to establish a single permanent Court Martial, covering all three Services, to replace the one-off courts martial that have previously had to be convened for each trial. The intention is that there should be "a single, harmonised system governing all members of the armed forces" (see para 16 of the explanatory notes to the 2006 Act (pdf version)).

Implementing the detail of the new Courts Martial system, the Courts-Martial (Army) Rules 2007, SI 2007 3442, the Courts-Martial (Royal Navy) Rules 2007, SI 2007 3442 and the Courts-Martial (Royal Air Force) Rules 2007, SI 2007/3444 replace the previous Courts-Martial Rules for each of the Services with effect from 1st January 2008. Full explanatory notes on the 2007 Courts Martial rules are available on the OPSI website and see generally notes at Specific employments/army, navy and air force/discipline acts .

The Act includes provisions for the appointment of a Service Complaints Commissioner and for his handling of allegations made to him that a person subject to service law has been wronged in a prescribed way (intended to cover complaints by service personnel of discrimination, harassment and bullying and of dishonest, improper or biased behaviour - the details are set out in Armed Forces Act 2006 s.338 and Armed Forces Act 2006 s.366 and in draft The Armed Forces (Service Complaints Commissioner) Regulations 2007).

Armed Forces Act 2006 s.334 provides that current and ex service personnel who think they have been wronged in any matter relating to their service, may make a "service complaint". DRAFT The Armed Forces (Redress of Individual Grievances) Regulations 2007 prescribes matters about which such a person may not make a service complaint.

The Act also has provisions to continue the application of service law to civilians (in particular dependants and contractors) accompanying the armed forces overseas (see in particular s.370 of, and sch 15 to, the Act).