Strontium (Sr) and calcium (Ca) isotopic compositions and Sr/Ca ratios have been analysed in different fractions of pedogenic needle fibre calcite (NFC) from the Swiss Jura Mountains (Villiers, Neuchâtel, Switzerland) in order to determine their Ca sources and to investigate the potential role of fungi in the origin of NFC. 87Sr/86Sr ratios have been measured to trace the Ca trapped within different pedogenic carbonate. This ratio was compared for previously identified microscopic morphological groups of NFC, the bulk soil fine earth (<2 mm), the carbonate host rock (CHR), a late calcitic cement (LCC, another pedogenic carbonate precipitated physicochemically at the same depth as NFC in soil pores), the soil solution, and the throughfall. The 87Sr/86Sr indicated a mixing of weathered allochthonous minerals (an atmospheric component) and the dissolved CHR (the local geogenic component). Moreover, the comparison of 87Sr/86Sr ratios of the different types of NFC with LCC suggests that the contribution of Ca from the main Ca sources slightly differs between NFC morphotypes and LCC. In addition, the three NFC morphotypes displayed Sr isotopic compositions different from each other, emphasizing a direct relationship between the microscopic shapes of NFC and the processes involved in their respective formation, including the origin of the Ca. Strontium concentrations and δ44/40Ca values of NFC and LCC crystals were used to determine possible differences in their growth rate and/or micro-environmental conditions during their formation. Crystals described micromorphologically as simple needles (SN) were enriched in 44Ca and depleted in Sr compared to LCC, suggesting that the elongated shape of the SN crystal cannot be related to a rapid precipitation rate, but rather to a slow precipitation. Calculations applied to the soil solution evolution during calcite precipitation demonstrates the utilisation of large portions of the Ca pool for NFC formation within a closed system, e.g. inside an organic mould, such as fungal hyphae. The differences between the three microscopic groups can be explained by a mixing of the SN with a LCC-like compound originating from the soil solution.