One of the most striking aspects of the biology of demosponges is their pervasive association with bacterial communities of varying diversity and composition. Together with the sponge host these communities form the sponge holobiont. First discovered and described in the late 1970s, the study of sponge-bacteria associations has evolved into a dynamic research field. To date, more than 40 bacterial phyla have been found in association with sponges, forming communities that are different from the bacterioplankton of the surrounding water and include sponges-specific bacterial associates. Despite the large body of information available on the diversity of the sponge microbiome, less is known about the molecular mechanisms used by sponges to interact with their bacterial symbionts and vice versa. Yet, studying how sponges interact with their microbiomes is pivotal to understanding how these systems react to changes in the environment and when these changes lead to a disruption of sponge-microbe associations. An important factor hampering the characterization of the sponge-microbiome molecular cross-talk mechanisms is the lack of broadly applicable molecular methods to, for instance, efficiently sequence meta-transcriptomes across a broad range of sponge species. To overcome this limitation, we implemented a hybrid-capture strategy capable of depleting both sponge and bacterial rRNA from total RNA extracts of highly divergent demosponges with microbiomes of different complexity. Our Pan-Demosponge rRNA depletion strategy allows for the efficient characterization of the metatranscriptome of diverse demosponge holobionts and the simultaneous quantification of gene expression in both the host and its microbiome.