In this work, an anomalous microscopic and macroscopic behavior during the hardening process of a calcium phosphate cement, based on anhydrous dicalcium phosphate, was observed. Indeed, the standard compressive strength measurements provided completely unexpected results, which encouraged a deeper investigation by means of X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron and atomic force microscopies. The energy dispersive X-ray diffraction mode was preferred to the conventional angular dispersive one, the former being particularly suitable for the real-time studies, allowing us to follow the hardening process in situ and to confirm that the investigated cement undergoes a long-time crystallization much more complex than expected. Indeed, the sequence of diffraction patterns exhibited anomalous intensity modulations (corresponding to structural changes taking place upon hardening) being consistent, and even in phase, with the variations of the compressive strength. These anomalous intensity modulations were confirmed also by the in situ time-resolved Fourier transform infrared spectroscopy. The explanation of the anomalous behavior was given by means of a multiscale approach correlating the microscopic (structural) and macroscopic (compressive strength) properties. In perspective, this finding may be interesting not only from the fundamental materials science point of view, but also for novel applications. For example, it might be utilized as an "intrinsic bioreactor", playing the role of stimulator of cellular proliferation by exerting stresses due to its alternative contracting and expanding internal forces on the tissues.