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Calcium carbonate from marble and seashells is an eco-friendly, sustainable, and largely available bioresource for producing natural bone-like calcium phosphates (CaPs). Based on three main objectives, this research targeted the: (i) adaptation of an indirect synthesis route by modulating the amount of phosphorus used in the chemical reaction, (ii) comprehensive structural, morphological, and surface characterization, and (iii) biocompatibility assessment of the synthesized powdered samples. The morphological characterization was performed on digitally processed scanning electron microscopy (SEM) images. The complementary 3D image augmentation of SEM results also allowed the quantification of roughness parameters. The results revealed that both morphology and roughness were modulated through the induced variation of the synthesis parameters. Structural investigation of the samples was performed by Fourier transform infrared spectroscopy and X-ray diffraction. Depending on the phosphorus amount from the chemical reaction, the structural studies revealed the formation of biphasic CaPs based on hydroxyapatite/brushite or brushite/monetite. The in vitro assessment of the powdered samples demonstrated their capacity to support MC3T3-E1 pre-osteoblast viability and proliferation at comparable levels to the negative cytotoxicity control and the reference material (commercial hydroxyapatite). Therefore, these samples hold great promise for biomedical applications.