The CCHR's procedures are governed by the CFHO and the CCHR's Rules and Regulations. The CCHR investigates complaints of discrimination by interviewing witnesses and reviewing documentary evidence. It uses its subpoena power, if necessary to compel testimony and the production of documents. Many cases also settled or are withdrawn during the investigative stage.

If, after an investigation, the Executive Compliance Staff of the Commission on Human Relations finds no substantial evidence of a violation, the case is dismissed. If it finds that there is substantial evidence of a violation, the CCHR may refer the case to mediation where an independent mediator hired by the CCHR will attempt to help the parties reach a resolution of the dispute. If the parties do not reach an agreement, the case proceeds to an Administrative Hearing Officer. At the hearing, both parties present their case to the Hearing Officer who makes recommended findings of fact, conclusions of law and appropriate relief, if any, after the hearing. The CCHR Board of Commissioners makes the final ruling after all hearings.