The management of soil fertility in organic greenhouse systems differs quite widely across Europe. The challenge is to identify and implement strategies which comply with the organic principles set out in (EC) Reg. 834/2007 and (EC) Reg. 889/2008 as well as supporting environmentally, socially and economically sustainable cropping systems. In this paper, written by a group of scientists of different geographical origin and with different background, the state of the art of the sector and the main characteristics of the European organic greenhouse cropping systems are described. The main bottlenecks and constraints are discussed with a particular reference to the regulatory framework in force. The most relevant issues that may influence the enforcement and future development of the sector have been identified as specific knowledge gaps. For each of them, the appropriate research needs were elaborated in a multidisciplinary perspective as forthcoming challenges for the whole sector. Although not exhaustive, given the wide heterogeneity of the implemented systems, this paper is able, for the first time, to give a structured outlook on soil fertility management in protected organic conditions on a European scale.