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The importance and functionality of the invoice document in combination with the growing need for efficiency, have led to its migration from paper to electronic form. The result of this evolution is the development of elnvoicing services, which enable commercially engaged enterprises and organizations to exchange, process and store invoices in an electronic form. The development of independent elnvoicing implementations creates significant interoperability issues. This paper focuses on the interoperability aspects of the SELIS service that is an open, practical, cost-effective and secure solution in accordance to EU legislation. The main objective of the paper is to present the methodologies and tools that have been used in order to test the service's interoperability aspects in three major areas of concern: electronic signatures, Web services and support for enterprise resource planning systems (ERPs).