The Foundation Board of the Krzyżowa Foundation consists of 22 people from various countries. It is elected for three years and meets twice per year in Krzyzowa. Ten of its members are delegates from organisations and associations with a special connection to Krzyzowa. Both the German and the Polish government send one representative.

The Foundation Board elects the Supervisory Board of the Foundation every three years. This body works on a voluntary basis and its members come from Germany, Poland or a third country. It consists of up to seven members.
The Supervisory Board counsels and monitors the management of the Foundation, consisting of three full-time representatives.

Work in Krzyzowa is supported by the committees of the Foundation Board. These committees include both employees of the Foundation and volunteers, and advise the respective departments: Advisory Board for the International Youth Meeting Centre (IYMC), European Academy and Memorial Site Commission, Volunteers Commission.

Detailed description of the tasks of the bodies may be found in the statutes of the Foundation.