Upper Jurassic phosphatic stromatolites associated with condensed pelagic sediments in Alpine-Mediterranean paleomargins mainly consist of microbially precipitated francolite, a low crystallinity carbonate fluorapatite. SEM images of microbial phosphate laminae show highly porous colloform textures formed by dense accumulations of micrometre-size spheroidal, ovoidal and sausage-shaped bodies that in places form strings and resemble bacterial growth structures. TEM observation reveals that these structures are mostly constituted by an arrangement of hexagonal crystallites of calcium phosphate, with sizes ranging between 0.1 and 1 μm in diameter, of the same shape and size as those observed in mature dental enamel. The phosphate crystallites are wrapped in Fe-Al-Si-rich poorly crystalline phases (authigenic Fe-rich smectite plus Fe-Si-Al-rich amorphous phases) that confer them the rounded external morphologies usually observed under SEM. TEM study also reveals the existence of rounded electron-lucent centres of 5–50 nm in diameter within these francolite crystallites, produced by the release of volatile compounds under electron bombardment. HRTEM study of some areas between francolite crystals and clays shows the presence of: (1) pools of extremely small, poorly crystalline calcium phosphate crystals with two ranges of sizes (20–50 nm and 5–15 nm in basal sections), some of them showing modulated contrast interpreted as growth steps; and (2) of an amorphous calcium phosphate. The amorphous phosphate phase constitutes a cloudy film that surrounds crystallites and sometimes forms groups of spherules with sizes ranging between 2–5 nm. Low crystallinity Fe-rich smectite, Fe-Si-Al-rich non-crystalline phases, amorphous calcium phosphate, and francolite appear so closely intergrown with each other that a genetic relation must be inferred for all of them. The observed textural and structural relationships demonstrate that, in the phosphate stromatolites, bacterially-mediated precipitation of an amorphous calcium phosphate precursory of the francolite crystals was associated with that of Fe-Si-Al-rich gels precursory of authigenic smectite. The precipitation of amorphous phases was kinetically favoured, and took place in close relation to bacterial mats and sheaths rich in mucilaginous organic substances, after heterotrophic bacterial degradation of P-rich organic matter. During early diagenesis amorphous phosphate precursors transformed into francolite.