The flavin derivatives 10‐methyl‐isoalloxazine (MIA) and 6-fluoro-10-methyl-isoalloxazine (6F-MIA) were encapsulated in two alternative metal-organic frameworks, (MOFs) MIL53(Al) and MOF5, using a post-synthetic, diffusion-based incorporation into microcrystalline MIL-53 powders and an in-situ approach during the MOF-5 synthesis. The flavin@MOF composites were analyzed by powder X-ray diffractometry (PXRD), N2-sorption studies and time-resolved fluorescence spectroscopy and microscopy. The maximum amount of flavin dye incorporation is 3.9 wt% for MIA@MIL-53(Al) and 1.5 wt% for 6F-MIA@MIL-53(Al), 0.85 wt% for MIA@MOF-5 and 27.6 wt% for 6F-MIA@MOF-5. The emission wavelengths of all flavin@MOF composites mostly correspond to the wavelengths of the flavins in solution. Time-resolved spectroscopy showed that the fluorescence lifetime of flavin@MOF of 2-4.7 ns also corresponds to those in solution but is significantly prolonged compared to the solid flavin dyes with less than 1 ns, thereby confirming the concept of "solid solutions" for dye@MOF composites. The fluorescence quantum yield (ΦF) of the flavin@MOF composites is about half of the solution but is significantly higher compared to the solid flavin dyes. Both the fluorescence lifetime and quantum yield of flavin@MOF decrease with the flavin loading in MIL-53. Theoretical calculations using plane-wave and QM/MM methods are in good correspondence with the experimental results and explain the electronic structures as well as the photoluminescence/photophysical properties of crystalline MIA and the flavin@MOF composites. In the solids flavins π-stacking interactions of the molecules lead to a charge transfer state with low oscillator strength resulting in aggregation-caused quenching (ACQ) with low lifetimes and quantum yields. In the MOF pores the flavin molecules are separated and the computed MIA@MOF structures do not find π-stacking interactions to the pore walls but only weak van-der-Waals contacts which reasons the enhanced fluorescence lifetime and quantum yield of the flavins in the composites compared to their neat solid state. The flexible MOF MIL-53(Al) was optimized essentially to the experimental large-pore form in the guest-free state with QuantumEspresso (QE) and with MIA molecules in the pores the structure contracted to close to the experimental narrow-pore form which was also confirmed by PXRD. In summary, the incorporation of flavins in MOFs yields solid-state materials with enhanced rigidity, stabilized conformation and reduced aggregations of the flavins, leading to increased fluorescence lifetime and quantum yield as controllable photo-luminescent and photo-physical properties.