Ensuring a consistent crystal structure over a wide temperature range can be desirable behaviour in organic devices. This study investigates a layered crystal system formed by hydrogen-bonded chloro-s-triazine rings functionalised with alkyl or fluoroalkyl chains between the layers. When substituted with N-propyl groups (C3), the crystal undergoes a thermally-induced phase transition where the chains are ordered and bent below 170 K and disordered and extended above 175 K. Replacement with fluorinated N-propyl chains (C3-F) produces the same layered crystal but successfully suppresses the phase transition. The hydrocarbon and fluorocarbon analogues were found to be incompatible and unable to form co-crystals from solution or with mechanical mixing. Both effects were ascribed to more attractive C-F…F-C and C-H…F-C interactions in the fluorinated analogue. Long perfluoroalkanes are well known for controlling assembly in the solid state, but this study suggests that short-chain fluoroalkanes can exert strong control over the assembly and stability of an organic crystal.