Synthetic clay analogues (SCAs) of a new organosilicate layered material family, in contrast to common clays, are produced via an in situ room-temperature sol–gel route, providing the possibility for the design and synthesis of diverse, tailor-made functional groups on the surface and interior of the synthetic clay sheets. In this work, we introduce organophyllosilicates bearing different functional end groups, which are synthesized by a magnesium metal salt precursor and organosilanes such as (3-aminopropyl)triethoxysilane (APTEOS), N-[3-(trimethoxysilyl)propyl]ethylenediamine (EDAPTEOS), N-(3-trimethoxysilylpropyl)diethylenetriamine (TAPTMOS), 1,4-bis(triethoxysilyl)benzene (BTB), tetraethyl orthosilicate (TEOS), 3-glycidoxypropyltrimethoxysilane (GLYMO), and (3-chloropropyl)trimethoxysilane (CPTMOS). The surface free energy for various organosynthetic clay analogues lies in the 29–252 mJ/m2 range. SCA’s antimicrobial activity was tested against both Gram-negative and Gram-positive bacteria to evaluate the effect of surface functionalization on the viability of these microorganisms. The amino-SCAs displayed higher antibacterial activity compared to epoxy-SCAs, presenting a dose-dependent effect and a structure-dependent motif. Furthermore, Gram-positive bacteria were more susceptible to SCA treatment than Gram-negative.