Crystallisation of barium carbonate in the presence of silica can lead to the spontaneous assembly of highly complex superstructures, consisting of uniform and largely co-oriented BaCO3 nanocrystals that are interspersed by a matrix of amorphous silica. The formation of these biomimetic architectures (so-called silica biomorphs) is thought to be driven by a dynamic interplay between the components, in which subtle changes of conditions trigger ordered mineralisation at the nanoscale. In particular, it has been proposed that local pH gradients at growing fronts play a crucial role in the process of morphogenesis. In the present work, we have used a special pH-sensitive fluorescent dye to directly trace these presumed local fluctuations by means of confocal laser scanning microscopy. Our data demonstrate the existence of an active region near the growth front, where the pH is locally decreased with respect to the alkaline bulk solution on a length scale of few microns. This observation provides fundamental and, for the first time, direct experimental support for the current picture of the mechanism underlying the formation of these peculiar materials. On the other hand, the absence of any temporal oscillations in the local pH – another key feature of the envisaged mechanism – challenges the notion of autocatalytic phenomena in such systems and raises new questions about the actual role of silica as an additive in the crystallisation process.