The phase preservation of synthetic C-S-H (Ca/Si = 0.8 and 1.5), ettringite, and hydrated LC3 paste under different preparation and storage conditions was assessed through X-ray diffraction. LC3 powder and slice samples (the latter, unpolished or polished using isopropanol or water) were either submitted to hydration stoppage (with isopropanol) or not (“fresh samples”). Results showed that non-vacuum storage preferentially carbonated hemicarbonate in the hydration-stopped LC3 sample, while fresh synthetic phases and LC3 samples experienced carbonation within minutes, affecting ettringite, hemicarbonate, portlandite, and C-S-H. The C-S-H fresh sample with the higher Ca/Si ratio was more sensitive to carbonation. Polishing the LC3 fresh slice with water partially solubilized portlandite, while polishing it with isopropanol led to the best phase preservation; the water-polishing procedure did not significantly harm phase preservation in the hydrated-stopped sample. Compared to powder samples, slice samples led to slightly more intense ettringite, hemicarbonate, and portlandite XRD peaks while reducing preferred orientation in LC3 paste. Overall, slice samples, when polished appropriately, proven to be the most suitable preparation method to preserve the crystalline hydrated phases in the LC3 system assessed. Care should be taken for fresh samples which can undergo carbonation within minutes.