Temporal changes in the composition and ultrastructure of hyaline walls of calpionellids during the Late Jurassic, coinciding with the massive increase of abundance of calcareous nannoplankton and with the onset of maiolica and biancone deposition, are poorly known. Here, we investigate the microtexture of pelagic deposits and the preservation, ultrastructure and chemical composition of three calpionellid genera in the upper Tithonian–lower Berriasian of the Kysuca–Pieniny and Orava successions (Pieniny Klippen Belt, Western Carpathians), using scanning electron microscopy (SEM), backscattered electron imaging (BSE), and wavelength-dispersive spectroscopy (WDS). The microtexture of these facies consists of interlocked pelagic skeletal remains and micritic or microsparitic pore-filling cements. Low-Mg calcitic calpionellid loricae and nannofossils are affected by (1) small-scale dissolution, which causes irregular and locally very thin wall thickness of loricae and (2) aggrading neomorphism, which produces coarser lorica crystals and results in the loss of inter-crystalline boundaries relative to the original lorica ultrastructure. In spite of these diagenetic effects, calpionellid genera differ in their test ultrastructure. Crystals in the hyaline layer of Praetintinnopsella and Crassicollaria are ~1 μm long and almost equidistant (length/width ratio ~1.3), whereas in Calpionella, they are ~2.2 μm long, more elongated (length/width ratio ~2), and oriented perpendicularly or obliquely to the inner surface of the lorica. The ultrastructure of the Praetintinnopsella hyaline layer more closely resembles that of Crassicollaria that of Calpionella, indicating a calcification trend characterised by the formation of larger crystals with lower surface area-to-volume crystal ratio. The loricae of these genera are enriched in Mg and S and impoverished in Mn relative to surrounding micritic and microsparitic grains. The initial diagenetic phase was represented by (1) dissolution of micro- and nannoplankton calcitic remains, (2) by precipitation of micritic and microsparitic cements within pore spaces among uncompacted skeletal particles and inside loricae, and (3) release of Mg from echinoderms coupled with microdolomite precipitation within ossicles or along syntaxial rims. This stage was followed by a phase with small-scale aggrading neomorphism, and ultimately by a late-diagenetic phase characterized by the precipitation of authigenic quartz and albite. Although dissolution, cementation and neomorphism probably reduced abundance of identifiable micritic fraction and abundance of dissolution-sensitive nannofossils, diagenesis did not obliterate differences in chemical composition between calpionellids and other components.