Mn-rich nanoscale secondary phases were identified in LiFe1-xMnxPO4, despite the known complete solubility for the LiFePO4-LiMnPO4 system and the observed linear increase in the lattice parameters of LiFe1-xMnxPO4 with increasing Mn concentration. Carbon free LiFe1-xMnxPO4 (x = 0, 0.05, 0.10, 0.25) were prepared by the sequential precipitation of Li3PO4 and (Fe1-xMnx)3(PO4)2, followed by hydrothermal treatment. At low doping concentration (x ≤ 0.05), Li-Mn-O secondary phases were discerned by Raman spectra, which corroborated with the inductively coupled plasma elemental analysis. Though energy dispersive elemental mapping with scanning transmission electron microscopy do not show segregation of Mn at low concentrations, Mn-rich phases were clearly discerned at high doping concentration (x = 0.25). The kinetics of Mn-rich phase formation during hydrothermal synthesis of carbon free LiFe1-xMnxPO4, which was attributed to the difference in the solubility constant of the intermediate products of Li3PO4 and (Fe1-xMnx)3(PO4)2, and its implications on the capacity of LiFe1-xMnxPO4 cathode material were discussed. Our results present how de-convoluted Raman peaks show clear signatures of nanophase impurity segregations and how an increase in the lattice constant with Mn doping concentration can be decisive.