Animal burrowers leave an indelible signature on the sedimentary record in most marine environments, with the seeming exception of low-oxygen environments. In modern sedimentary settings, however, sub-millimetre-sized benthic animals (meiofauna) are adapted to low oxygen and even sulfidic conditions. Almost nothing is known about their impact on ancient marine sediments because they leave few recognizable traces. Here we show, in classic Pliocene-aged anoxic facies from the Mediterranean, the first reported trace fossil evidence of meiofaunal activity and its relation to changing oxygenation. A novel approach utilizing electron imaging of ion-polished samples shows that meiofauna pervasively reworked sediment under oxygen-depleted conditions that excluded macrofauna, fragmenting organic laminae and emplacing 15- to 70-μm-diameter faecal pellets without macroscopically influencing the fabric. The extent of reworking raises the question: how pervasively altered are other sediments presently assumed to lack animal influence and how far into the geological record does this influence extend?