In this work, we report the synthesis and structural characterisation of the ligand 2-(pyridin-3-yl)-benzo[de]isoquinoline-1,3(2H)-dione, 5, its isostructural Werner complexes ML4(NCS)2 (L = 5; M = Co(II) and Ni(II)), and five clathrates with three aromatic guests, ML4(NCS)2·2G (M = Co(II) and Ni(II), G = nitrobenzene (NB); M = Co, G = 1,2-dichlorobenzene (1,2-DCB); M = Co(II) and Ni(II), G = o-xylene (OX)). 5 was prepared in high yield by condensation in the solid-state (C3S3, Cocrystal Controlled Solid-State Synthesis). The Werner complexes ML4(NCS)2 (M = Co(II) and Ni(II)) (apohosts) were prepared by reacting M(NCS)2 (M = Co(II) and Ni(II)) and 5 in 1-butanol at 60 °C for 24 h. The Werner clathrates were prepared by reacting M(NCS)2 (M = Co(II) and Ni(II)), G and 5 in 1-butanol at 60 °C for 48-96 h. The clathrates were observed to transform to the apohost ML4(NCS)2 upon heating. CoL4(NCS)2·2NB was subsequently regenerated by exposing CoL4(NCS)2 to liquid NB at 60 °C for 48 h. This phase change occurred as a single-crystal to single-crystal phase transformation and was studied by single crystal X-ray diffraction, powder X-ray diffraction and thermal analyses. Structural analyses of the apohost CoL4(NCS)2 and its Werner clathrate CoL4(NCS)2·2NB indicated that rotational freedom of the Co-N bonds together with torsional flexibility of the ligand between the imide bond and the pyridine moiety are key to enabling the structural switching induced by exposure to NB or its removal.