The scientific community needs tools to harness the potential of data in the field of environmental biotechnology, ensuring that these data complies with the principles of Findable, Accessible, Interoperable, and Reusable (FAIR) data management. Here we introduce two information systems developed at INRAE: On one hand, EnviBIS [1], Environmental Biorefinery Information System is an ontology-driven information system for managing bioprocess data in an environmental biorefinery context, using the OpenSILEX [2] open-source software suite. This system handles the acquisition of heterogeneous data from sensors, observations or analytical devices, as well as on-line data management and bioprocess monitoring. The core ontology of OpenSILEX is based on standards ontologies (e.g. Dublin Core, FOAF, SOSA, PROV-O). It has been extended to specialize the EnviBIS tool by domain ontologies such as the Environmental Biorefinery Ontology (EBO) which, coupled with the Process and Observation Ontology (PO2), enables the description of biological and physical transformation processes. On the other hand, DeepOmics [3] is an information system designed to store meta-omic data pertaining to environmental biotechnology processes. It enables storing and, in the future querying, cross-referenced amplicon sequencing data, to metadata associated with samples from lab-scale reactors, pilots, or industrial sites. The aim of DeepOmics is to create a comprehensive framework for leveraging meta-omic data and metadata. The interoperability between these two tools is currently under development. It will enable researchers to access and analyze data from heterogeneous sources, thus promoting interdisciplinary knowledge aggregation. A demonstration is planned, to illustrate in concrete terms the added value of our approach regarding ease of use and efficiency in data processing, in the field of environmental biorefinery.