In recent years, there has been a significant focus on coral habitats, encompassing both shallow and deep ecosystems. Historically, most studies concentrated on scleractinian corals, however contemporary research acknowledges the ecological importance of octocoral species, and the need to improve our understanding of their biology. Histology, which describes the internal morphology of animal tissues, is an essential tool for a wide range of biological studies, including reproductive biology, life history, taxonomy and phylogeny. Processing octocoral tissue histologically can be a complex task, given the unique skeletal structure of these organisms. Octocorals have internal skeletal structures called sclerites, which are composed of calcium carbonate and are embedded into the coral tissue. Decalcification of these structures creates air pockets in the tissue that hault further histological processing. Moreover, many octocorals possess a skeletal axis that is predominantly composed of organic matter, but may contain varying degrees of calcium carbonate. Including the axis in histological analysis may require experimentation to adjust the processing times. Although several studies report processing times for histological analysis, it is difficult to find detailed information on how to process octocoral tissue. Here, we present a detailed protocol that separates octocoral polyps from the skeletal axis, and utilizes vacuum to address issues with decalcification. The use of single polyps, or small polyp groups, decreases the processing time, and allows for manual processing without the use of automated systems. Vacuum removes trapped air from decalcification and increases the quality of the histological sections. We also include an optional step for specimens that were directly preserved in ethanol without prior fixation. Lastly, we demonstrate simple ways to section paraffin blocks that do not require extensive experience in histological sectioning.