Although environmental factors such as grain size and organic carbon content may influence the distribution of microbes in marine sediments, there has been little experimental study of the topic to date. To investigate how those sediment variables affect microbial colonisation under in situ conditions, deep-sea sediments and artificial sediments (glass beads, sands) were incubated in the Arctic deep sea at 2500 m water depth with or without chitin, one of the most important carbon polymers in marine environments. Microbial abundance, biomass, chitobiase activity and changes in community structure were monitored after 7 days and 1 year. In control sediments without chitin addition, no significant changes in microbial abundance, biomass and activity were observed after 1 year. In the presence of chitin, however, considerable increases in these parameters were recorded in all three sediment types tested. Regardless of chitin addition, natural deep-sea sediments were always associated with higher values of microbial abundance, biomass and activity compared with artificial sediments. Sediment type was always found to be the most significant factor explaining variation in enzymatic activity and bacterial community structure as compared to the effects of chitin amount, incubation time, and changes in cell number or biomass. Overall, this is the first in situ study that has addressed the effects of multiple factors and their interactions on abundance, biomass, activity and community structure of microbial communities in the deep Arctic Ocean.