The work of the TRC was accomplished through three committees:
• The Human Rights Violations Committee investigated human rights abuses that occurred between 1960 and 1994.
• The Reparation and Rehabilitation Committee was charged with restoring victims' dignity and formulating proposals to assist with rehabilitation.
• The Amnesty Committee considered applications from individuals who applied for amnesty in accordance with the provisions of the Act.

Public hearings of the Human Rights Violations Committee and the Amnesty Committee were held at many venues around South Africa, including Cape Town (at the University of the Western Cape), Johannesburg (at the Central Methodist Mission), and Randburg (at the Rhema Bible Church).

The commission was empowered to grant amnesty to those who committed abuses during the apartheid era, as long as the crimes were politically motivated, proportionate, and there was full disclosure by the person seeking amnesty. To avoid victor's justice, no side was exempt from appearing before the commission. The commission heard reports of human rights violations and considered amnesty applications from all sides, from the apartheid state to the liberation forces, including the African National Congress.
The Commission found that there were 7,000 political deaths under Apartheid between 1948 and 1989. More than 19,050 people had been victims of gross human rights violations. An additional 2,975 victims were identified through the applications for amnesty. In reporting these numbers, the Commission voiced its regret that there was very little overlap of victims between those seeking restitution and those seeking amnesty.

A total of 5,392 amnesty applications were refused, granting only 849 out of the 7,111 (which includes the number of additional categories, such as "withdrawn").

The TRC's emphasis on reconciliation was in sharp contrast to the approach taken by the Nuremberg trials and other de-Nazification measures. South Africa's first coalition government chose to pursue forgiveness over prosecution, and reparation over retaliation.

Opinions differ about the efficacy of the restorative justice method (as employed by the Truth and Reconciliation Commission) as compared to the retributive justice method, of which the Nuremberg trials are an example. In one survey study, the effectiveness of the TRC was measured on a variety of levels:
• Its usefulness in terms of confirming what had happened during the apartheid regime ("bringing out the truth")
• The feelings of reconciliation that could be linked to the Commission
• The positive effects (both domestically and internationally) that the Commission brought about (i.e. in the political and the economic environment of South Africa).
In the study by Orlando Lentini, the opinions of three ethnic groups were measured in this study: English-speaking White South Africans, the Afrikaners, and the Xhosa. According to the researchers, all of the participants perceived the TRC to be effective in bringing out the truth, but to varying degrees, depending on the group in question.

The differences in opinions about the effectiveness can be attributed to how each group viewed the proceedings. Some viewed them as not entirely accurate, as many people would lie in order to keep themselves out of trouble while receiving amnesty for their crimes. (The commission would grant amnesty to some with consideration given to the weight of the crimes committed.) Some said that the proceedings only helped to remind them of the horrors that had taken place in the past when they had been working to forget such things. Thus, the TRC's effectiveness in terms of achieving those very things within its title is still debatable.