The fabric of sedimentary rocks in lacustrine archives usually contains long and continuous proxy records of biological, chemical and physical parameters that can be used to study past environmental and climatic variability. Here we propose an innovative approach to sedimentary facies analysis based on a coupled geomicrobiological and sedimentological study using high-resolution microscopic techniques in combination with mineralogical analyses. We test the applicability of this approach on Lake Son Kul, a high alpine lake in central Tien Shan (Kyrgyzstan) by looking at the mineral fabric and microbial communities observed down to the nanoscale. The characterization of microbe–mineral interactions allows the origin of four carbonate minerals (e.g. aragonite, dolomite, Mg-calcite, calcite) to be determined as primary or diagenetic phases in Lake Son Kul. Aragonite was mainly of primary origin and is driven by biological activity in the epilimnion, whereas diagenetic minerals such as Mg-calcite, calcite, dolomite and pyrite were triggered by bacterial sulphate reduction and possibly by methanotrophic archaea. A new morphotype of aragonite (i.e. spherulite-like precursor) occurs in Unit IV (c. 7100–5000 cal. BP) associated with microbial mat structures. The latter enhanced the preservation of viral relics, which have not yet been reported in Holocene lacustrine sediments. This study advocates that microbe–mineral interactions screened down to the nanoscale (e.g. virus-like particles) can be used successfully for a comprehensive description of the fabric of laminated lake sediments. In this sense, they complement traditional facies sedimentology tools and offer valuable new insights into: (1) the study of microbial and viral biosignatures in Quaternary sediments; and (2) palaeoenvironmental reconstructions.