Two-photon lithography technology has revolutionized the fabrication of 3D-structures from photoreactive materials by providing high precision and almost unlimited design freedom. Here, a zirconium-based metal-organic framework (MOF) based on benzophenonedicarboxylate (bzpdc) linker molecules has been micro-structured by a laser-induced chemical modification. Via a post-synthetical loading of the porous crystals with appropriate organic compounds and a subsequent femtosecond laser-induced two-photon absorption (TPA), a cross-linking of organic compounds with MOF’s bzpdc-linker is triggered. As a result, a precise functionalization of the material is achieved, leading to a permanent change in properties such as refractive index. With this work a significant step forward for 3D-tailoring material properties and manufacturing tuneable functional optical micro-devices is made.