Authigenic clays in close textural relation to carbonate fluorapatite within finely laminated phosphate stromatolites of Upper Jurassic age have been studied using scanning electron microscopy (SEM), transmission electron microscopy (TEM) and analytical electron microscopy (AEM). Stromatolite laminae consist of hexagonal prisms of francolite (sizes ranging between 0·1 and 1 μm) that are surrounded by poorly crystalline smectite and amorphous Fe–Si–Al oxyhydroxides. Microanalyses show that smectite is Fe rich, with highly variable composition, particularly regarding Fe and Si contents. Smectite has significant beidellitic, montmorillonitic and non‐tronitic substitutions. Although the lack of fringe contrast in some areas adjacent to the smectite packets with 1·0–1·3 nm spacing is due to differences in orientation of layers, textural and analytical data clearly indicate the presence of Fe–Si–Al amorphous phases intimately intergrown with smectite. The occurrence of poorly crystalline smectite and associated amorphous phases within microbially precipitated stromatolite laminae, both as envelopes around, and as pore‐fillings between extremely small calcium phosphate crystals, demonstrates authigenic smectite growth from a precursor Fe–Si–Al amorphous material. This material is formed in close association with a phosphate‐rich precursor. The textural and structural relations, the preservation of chemical precursors of glauconite such as nontronitic montmorillonite, and the presence of Fe–Si–Al amorphous mineral phases, imply crystallization of the observed crystalline phases from synsedimentary (bacterially precipitated) amorphous precursors during early diagenesis in postoxic environments. Carbonate fluorapatite was the first phase to crystallize from the primary gel; smectite and associated amorphous Fe–Si–Al oxyhydroxides were the residual material of the crystallization process. The slow rate of transformation (at low temperatures) from Fe–Si–Al‐rich gels to smectite, explains the textural relations between the poorly crystalline phases and the phosphate crystals, as well as the preservation of amorphous substances in relation to clays. Authigenic smectite represents the first step in glauconitization.