Burrowing and feeding benthic invertebrates generate various biogenic sediment structures. Such bioengineering is associated with a re-location of nutrients and, in most cases, with a disruption of the benthic community. We investigated the effects of different morphotypes of small-scale biogenic structures on the distribution and activity of bacteria in Arctic deep-sea sediments. Bacteria showed highly variable abundances, cellular biomasses and activities (estimated by thymidine and leucine incorporation) as a result of interacting driving forces: (i) Laterally transported organic particles accumulate at small-scale sediment elevations and depressions. (ii) Organic material is left behind crawling organisms as mucus or faeces. (iii) A significant proportion of bacteria is removed by predation or sediment relocation. In this context, the uppermost sediment layer beneath burrows and plough traces contained less bacteria of higher cellular biomass. Any nonconformity with biomass synthesis from organic compounds probably indicates a community shift because of sediment disturbance. Macrofaunal crawling and feeding tracks were shown to favour bacteria, both in abundance and cellular biomass. A high spatial patchiness along the track courses is suggested to depend on the availability of macrobenthic, metabolic products, as confirmed by faecal castings stimulating bacterial activity. This variable and highly complex scenario of microspatial bacterial community dynamics points to the potential of benthic fauna to cause habitat heterogeneity and to create micro-scale ‘hot spots’ at the deep seafloor.