Lithium- and manganese-rich (LMR) layered oxides are promising high-energy cathodes for next-generation lithium-ion batteries, yet their commercialization has been hindered by a number of performance issues. While fluorination has been explored as a mitigating approach, results from polycrystalline-particle-based studies are inconsistent and the mechanism for improvement in some reports remains unclear. In the present study, we develop an in situ fluorination method that leads to fluorinated LMR with no apparent impurities. Using well-defined single-crystal Li1.2Ni0.2Mn0.6O2 (LNMO) as a platform, we show that a high fluorination level leads to decreased oxygen activities, reduced side reactions at high voltages, and a broadly improved cathode performance. Detailed characterization reveals a particle-level Mn3+ concentration gradient from the surface to the bulk of fluorinated-LNMO crystals, ascribed to the formation of a Ni-rich LizNixMn2-xO4-yFy (x > 0.5) spinel phase on the surface and a spinel-layered coherent structure in the bulk where domains of a LiNi0.5Mn1.5O4 high-voltage spinel phase are integrated into the native layered framework. This work provides fundamental understanding of the fluorination effect on LMR and key insights for future development of high-energy Mn-based cathodes with an intergrown/composite crystal structure.