Research on biodiversity, its relation to ecosystem functioning and services, and the assessment of the impacts of environmental change on biodiversity needs an interdisciplinary perspective. This implies a great diversity of data and data formats gathered mostly in short- to mid-term collaborative research projects. It has been common practice that projects develop specific data management and communication solutions. We compare solutions of two major German collaborative research programs in functional biodiversity research to derive functional commonalities. This in-depth analysis follows five categories of the data life cycle: (i) data acquisition, (ii) metadata management, (iii) database, (iv) exploration, analysis and visualization, and (v) data curation and preservation. The results show that even though both systems were developed completely independently, they reveal comparable overall features and a similar state of implementation. Major focus areas lie in the implementation of comparable metadata schemas and their importance for storage and access strategies for tabular data on the value level. Basic analysis tools and similar management functions are considered. Intensive communication with the users and the orientation of ongoing developments based on user requirements is also important. Both systems are different mostly in specific details which, however, do not influence the overall comparable performance. It should be also emphasized that the same functionality is achieved with completely different software. The choice of software is based on the evaluation of available technologies. Thereby it might be influenced by individual experiences of the developers, but is mainly determined by the data diversity, which forces the usage of flexible technologies to develop adaptable systems. It is concluded that overall features for project databases of collaborative research projects must be supplemented by sophisticated data description, storage, and analysis structures to serve the requirements of integrative functional biodiversity research.