Serpentinization is known to provide substantial amounts of energy in the form of molecular hydrogen along with a suite of abiotic organic compounds of low molecular weight (mainly as short chain alkanes and carboxylic acids), all sustaining the development of microbial ecosystems in the mantle-derived crust. The latter have a cryptoendolithic life style and are responsible for (i) the local formation of biomass and of organic metabolic byproducts and (ii) the production of extracellular polymeric substances which organize the community in the form of a biofilm at the surface of the rock-forming minerals. In accordance, whatever their origin, organic compounds can be diverse and widespread in the shallow oceanic crust where they undergo hydrothermal degradation and remobilization through fluid circulations. Here we show that organic carbon is directly involved in low temperature serpentinization reactions (< 200 °C). Fine scale investigations of microbial niches hosted in serpentinites from the Mid-Atlantic ridge were performed using scanning and transmission electron microscopy along with scanning transmission X-ray microscopy. They suggest that organic coatings at mineral surfaces may influence the nature and structure of the serpentinization products as well as the mobility and speciation of transition metals as the reaction progresses. This likely constitutes an efficient yet poorly considered mechanism in active serpentinizing systems with possible implications for ore formation associated with the alteration of ophiolitic massifs and subsurface storage.