This work focuses on the effect of decompression on bacterial communities from deep-sea surface sediments. We evaluated the effects of slow and fast decompression (within hours and seconds, respectively), and repeated de-re-compression (up to 10 times) on the abundance and extracellular enzymatic activity of bacterial communities as well as their taxonomic composition using next generation sequencing of the 16S rRNA and rRNA gene. Decompression due to sample retrieval from the seafloor with a push corer or a pressure corer showed minor effects on bacterial cell numbers and enzymatic activity patterns. It however showed an initial effect on bacterial activity patterns based on 16S rRNA (cDNA) community analysis. This signal vanished during a few hours standing at atmospheric pressure. The results reported here may be useful to provide ideas for future research as to how bacterial communities react to the procedure of sample retrieval from a high pressure environment.