Synthesis of manganese citrates was carried out in the presence and absence of fluoride ions. The presence of HF or NaF led to the formation of new layered manganese citrates whose crystal structures were determined by single-crystal X-ray diffraction. The prepared single-phase citrates with and without fluoride ions were then used as precursors for the preparation of mesoporous MnxOy and hierarchically porous MnxOy@C phases, which could be of interest for catalytic, sorption, and electrochemical applications.