Deep-sea ecosystems have been characterised in many ways, such as deserts, stable, monotonous, poor, remote. Building on knowledge over the years, we now know that these extreme environments are highly variable and diverse hosting rich benthic communities that are largely affected and structured by food availability and quality. In the land-locked, oligotrophic Mediterranean Sea, food supply to the deep sea is expected to be dependent on pelagic production but also to be affected by inputs from the surrounding landmasses. Having this in mind, we used samples collected during the LEVAR expedition on board R/V METEOR (M71/2, winter 2006–2007) from two distinct deep-sea areas in the Levantine Sea for describing meiobenthic communities in relation to factors that may drive their spatial distribution, variability and patchiness at several scales. Area 1 (within the Pliny Trench) is located close to the island of Crete at ca 4000 m depth, whereas Area 2 (within Herodotus Abyssal Plain) is more distant from the island but shallower (ca 2700 m). Independent multiple-corer deployments performed at three stations within each area, the use of several sediment cores from each deployment, and the vertical sectioning of one sediment sample per deployment, allowed to explore meiobenthic patterns at multiple scales. A set of permutational analyses indicated differences between the two areas in terms of sedimentary food proxies that were coupled with corresponding differences in meiofauna richness, composition, and in abundances of the two most dominant meiobenthic metazoans, i.e. nematodes and copepods. Though to a lesser extent, variability in meiobenthic characteristics was also detected within and among stations. A similar trend was not clearly evident within deployments. Changes in meiofauna distribution occurred in relation to sediment depth layer as well, with evidence that the meiofauna vertical profile may differ between the two areas. Overall, our study shows that higher meiobenthic variability in the eastern Mediterranean deep sea is accounted for at the scale of area/habitat. Inferences of our results in light of previous findings in the same area imply that the relationship between food and meiobenthic composition could not be attributed to bathymetry or distance from the land, but is more probably explained by the high complexity and dynamics of trench habitats and their role as depositional environments acting as physical traps of organic material.