The society is administered by a Council appointed by the General Assembly of the society, which gathers every second year in connection to the SPPS congress. The location of assemblies alternates between the Denmark, Finland, Norway and Sweden, which are all represented in the Council. The composition of Council has varied over the decades and currently consists of President, Vice-presicent, Treasurer, Secretary general, Journal responsible, and PhD/Postdoc representative, in addition to two ordinary council members.
The presidency of the society rotates between the countries and there is a limit on the number of times a person can be elected President. Traditionally, the President, Secretary general, and Treasurer were elected from the same country, and the SPPS office moved accordingly between countries. This changed in 2015 when the Council decided to establish a permanent office in Lund (Sweden) with an employed Society secretary.
The journal Physiologia Plantarum has been an integral part of the society from the beginning with an appointed editorial board from the first adminstration in 1948. From 1976, a separate Journal committee was established to govern the journal. This committee was dissolved in 2005 whereafter one member of the council is elected as Journal responsible. Editorial tasks of the journal have always been carried out in Lund despite the fact that the current editor-in-chief and a part of the editorial team work from other locations.