Septarian concretions in the Staffin Shales Formation (Kimmeridgian, Isle of Skye) allow controls on concretion rheology and septarian cracking to be investigated. Stratabound concretions consist of anhedral ferroan calcite microspar enclosing clay and minor pyrite. Intergranular volumes range from 77% to 88%, and calcite δ13C and δ18O values in most concretion bodies range from −10·0‰ to −17·3‰ and +0·3‰ to −0·6‰ respectively, consistent with rapid and pervasive cementation in marine pore fluids. Septarian rupture occurred during incipient cementation, with a sediment volume reduction of up to 43%. Crack-lining brown fibrous calcite records pore fluid re-oxygenation during a depositional hiatus, followed by increasing Fe content and δ13C related to bacterial methanogenesis. Brown colouration results from an included gel-like polar organic fraction that probably represents bacterially degraded biomass. A new hypothesis for concretion growth and septarian cracking argues that quasi-rigid ‘proto-concretions’ formed via binding of flocculated clays by bacterial extracellular polysaccharide substances (EPS). This provided rheological and chemical conditions for tensional failure, subcritical crack growth, volume contraction, calcite nucleation, and incorporation of degraded products into crack-lining cements. Bacterial decay of EPS and syneresis of host muds provided internal stresses to initiate rupture at shallow burial. Development of septarian (shrinkage) cracks in muds is envisaged to require pervasive in situ bacterial colonization, and to depend on rates of carbonate precipitation versus EPS degradation and syneresis. Subsequent modification of septarian concretions included envelopment by siderite and calcite microspar, hydraulic fracturing associated with Cretaceous shallow burial or Palaeogene uplift; and cementation by strongly ferroan, yellow sparry calcite that records meteoric water invasion of the host mudrocks. An abundance of fatty acids in these spars indicates aqueous transport of organic breakdown products, and δ13C data suggest a predominantly methanogenic bicarbonate source. However, the wide δ18O range for petrographically identical cement (−1·3‰ to −15·6‰) is difficult to explain.