In this study, the ISO 17065:2012 Conformity Assessment—through comparisons between the required standards for organizations that provide certifications towards products, processes, and services, and the programs regarding the certification of organic agricultural practices in Turkey that are regulated by Turkish Regulations on Principles and Implementation of Organic Agriculture, some recommendations are developed for applications in similar countries, by investigating the similar or contradictory issues surrounding the conformity assessment activities with the regulations published in this field. To contribute to the management and improvement of the certification and accreditation processes of the conformity assessment bodies carrying out the certification activities of the agricultural certification programs within the scope of the ISO 17065:2012 standard, the degree of compliance has been identified by comparing the requirements of the Regulations on the Principles and Implementation of Organic Agriculture. The compatibility of these documents and the absence of conflict in these practices will provide a sense of confidence for all relevant parties, including consumers benefiting from the organic market. According to the conclusions of this evaluation, comparison results were interpreted, taking into account the degrees of compliance from the perspectives of the Ministry of Agriculture and Forestry of the Republic of Turkey that carries out the provisions of the Regulation on the Principles and Implementation of Organic Agriculture, the Turkish Accreditation Agency (TURKAK) that carries out accreditation activities according to the Regulation, and the certification bodies that are the implementers of the standards mentioned above and regulations, the problem areas were determined, and recommendations have been developed. The national problems in this context have been specified, and recommendations were developed based on observations and examinations of ISO 17065:2012 international standard.