Herein, bio-compatible self-assembled peptide fibrils have been developed for adsorption of organic pollutants for water remediation with high adsorption capacity. The different morphological motifs of self-assembled dipeptide Fmoc-FW-OMe was formulated using solvent modulation which was characterized by optical microscopy, SEM, XRD and FT-IR. Specifically, the fibril structures were used for selective adsorption of cationic dyes from aqueous solutions with exceptional adsorption capacity noted for crystal violet (625 mg/g). To understand the mechanism of dye adsorption, kinetics studies and adsorption isotherm studies were carried out which proved that the adsorption follows second order kinetics and Langmuir adsorption isotherm. The pH studies suggested that the adsorption of dye is much higher in alkaline conditions as compared to acidic conditions. The self-assembled peptide fibrils showed high reusability over five cycles with negligible effect on the dye adsorption capacity. Notably, this is the first report that discusses the application of self-assembled short peptide based fibrils for removal of dyes from waste water and in particular, it demonstrates the highest adsorption capacity reported for crystal violet dye so far. In general, this efficient capturing of dye pollutants with minimum usage of biocompatible adsorbents presents a simple and cost effective method for water remediation.