Crystalline porous materials, especially inorganic porous solids such as zeolites, usually have negative frameworks with extra-framework mobile cations and are widely used for cation exchange. It is highly desirable to develop new materials with positive frameworks for selective anion exchange and separation or storage and delivery. Recent advances in metal-organic framework synthesis have created new opportunities in this direction. Here we report the synthesis of a series of positive indium metal-organic frameworks and their utilization as a platform for the anion exchange-based separation process. This process is capable of size- or charge-selective ion-exchange of organic dyes and may form the basis for size-selective ion chromatography. Ion-exchange dynamics of a series of organic dyes and their selective encapsulation and release are also studied, highlighting the advantages of metal-organic framework compositions for designing host materials tailored for applications in anion separation and purification.