Stable isotope probing (SIP) of isotopically labelled RNA is well-established in environmental microbiology. The concept of a labelling-based detection of process-relevant microbes independent of cellular replication or growth allows for a direct handle on functionally relevant microbiome components. Although applied mostly for rRNA, RNA-SIP also holds the potential to detect labelled environmental transcripts, providing a targeted access to process-relevant gene expression in complex systems.