New morpholinium surfactants with a carbamate fragment between the amphiphile head group and its hydrophobic tail (CnMB-carb, where n = 8, 10, 12, 14, 16) were synthesized. The cmc values obtained by tensiometry for dodecyl, tetradecyl, and hexadecyl homologues are 3–4 times lower than those of 4-alkyl-4-methylmorpholinium bromides. The introduction of a carbamate fragment can be considered as tool for controlling cmc values. The calculation of the thermodynamic parameters of micellization, i.e., Gibbs free energy of micellization (∆Gmic), enthalpy of micellization (ΔHmic), entropy of micellization (ΔSmic), were carried out based on the temperature dependences of specific electrical conductivity as a function of surfactant concentration. It was determined that the aggregation of cationic surfactants is driven by the entropy and ΔG(CH2) is equal to 3.26 kJ/mol. The cmc values determined by fluorimetry were approximately two times lower than those obtained by tensiometry and conductometry, probably due to the ability to identify premicellar aggregates. Using the spectrophotometry, a twofold increase in the solubilization capacity of C16MB-carb (0.036 molOOT/molsurf) was established in comparison with a non-functionalized morpholinium surfactants with the same tail length (0.019 molOOT/molsurf). The “closed bottle test” showed that the degree of CnMB-carb biodegradation reaches 56.7–62.3%. It was found that the antimicrobial activity of the surfactants increases with the lengthening of the hydrocarbon tail with maximum activity for the tetradecyl homologue. In addition, dose-dependent activity of C14MB-carb and C16MB-carb on the cell wall, cell membrane, and membrane potential of Staphylococcus aureus was shown.