A new method combining micro-X-ray computed tomography (μXCT) and volumetric digital image correlation (V-DIC) in conjunction with in-situ mechanical testing was used to probe three-dimensional (3D) deformation behavior in a friction stir blind rivet (FSBR) joint of carbon fiber reinforced polymer (CFRP) composite. Intrinsic microstructural features such as fibers, pores and metal inclusions enabled accurate volumetric strain calculation of dense fiber reinforced polymer composites using V-DIC without the need for highcontrast additives. Deformation calculated with V-DIC was employed to determine variation of local mechanical properties within the FSBR altered stir-zone microstructure. Unique deformation mechanisms such as internal interfacial shear and microstructure-dependent local buckling were observed in situ. The obtained 3D microscale strain maps revealed that the deformation behavior in joint-affected zones was fundamentally different from that of the bulk composite. Combined μXCT and V-DIC were shown to be effective for understanding 3D microscale deformations in composites.