Anisotropy of magnetic susceptibility (AMS) has been widely used to infer magmatic flow patterns of granitoids where an appropriate AMS axis is parallel to an alignment of mafic minerals or magnetite. The magmatic flow fabric in Cretaceous granitic plutons from northeastern Japan was verified using an analysis of anisotropy of partial anhysteretic remanent magnetization (ApARM) which further isolates the magnetite subfabrics according to magnetite grain size. The preferred orientation of polysynthetic twins in plagioclase laths and clinopyroxene is discordant with the bulk AMS fabric along outer marginal zones of the granitoid, as shown by image analysis of microphotographs from thin sections cut in orthogonal planes. This suggests that the uncorroborated use of bulk AMS to detect flow fabric in granitoids has risks. Scanning electron microscopy (SEM) reveals that submicroscopic, needle-shaped magnetite inclusions exsolved in anhedral plagioclase and clinopyroxene may explain such anomalous exceptions to the validity of AMS fabrics. Our ApARM measurements show that the ApARM alignment of relatively high-coercive, submicroscopic magnetite inclusions is concordant to the linear orientation of anhedral plagioclase and clinopyroxene. The combination of SEM, AMS, and ApARM was required to confirm the magmatic and submagmatic flow pattern of granitoids in this study and is generally preferable to the use of AMS alone.