A new inclusion compound consisting of a guanidinium 1,3,5-tri(4-sulfophenyl)benzene (G3TSPHB) host framework containing isophorone guests that surround isolated and seemingly inaccessible pockets was amenable to guest exchange with hexafluorobenzene (HFB) through a single crystal-single crystal transformation (SCSCT). Single-crystal X-ray diffraction of intermediate transformation states, from the parent compound G3TSPHB·(isophorone)3.7·(methanol)5.4 to the final state G3TSPHB·(isophorone)3.1·(HFB)2·(methanol)2, indicated a crystal symmetry change from monoclinic to hexagonal prior to full incorporation of HFB. Optical microscopy during the SCSCT revealed the formation of lamellae, which expanded and then coalesced into a single crystal when the phase transformation was complete. In situ Raman microscopy revealed changes in the orientation of isophorone guests during the transformation that suggested a pathway for HFB entry into the host cavities. The SCSCT occurs more rapidly than expected on the basis of simple diffusion, consistent with facilitated transport along the lamellae interfaces and a reduction in the length scale for guest exchange.