Here, we present a novel approach for the analysis of fibril stability by chemical depolymerization which combines the advantages of both categories. Our method utilizes flow-induced dispersion analysis (FIDA) for separation of monomers from fibrils and quantification of monomer concentration within a thin fused-silica capillary. The approach is rapid, fully automated, amenable to high throughput, label-free, utilizes a commercially available instrument, and uses minute amounts of sample. We demonstrate its advantages by benchmarking it against four commonly used techniques using αSyn and PI3K-SH3 fibrils as the test cases. Using our newly developed approach we compare stability of fibrils at different experimental conditions and quantify thermodynamic stability differences between distinct fibril polymorphs. We believe that our new method is a versatile and useful tool for probing rugged amyloid landscapes in a quantitative, and efficient manner.