Plant secondary metabolites including phenolics and flavonoidsare synthesized through phenylpropanoid and phenylpropanoid-acetate pathways and significantly contribute against adverse effect of abiotic and biotic stresses. Herein, we present the development and execution of a novel and expeditious ultra-performance liquid chromatographic-photodiode array (UPLC-PDA) method for qualitative and quantitative analysis of 28 phenolic compounds comprising of flavonoids, phenolic acids, aldehydes and alcohols. The method is able to separate phenolic compounds in just 17 minutes with the separation of isobaric species such as 3,4 dihydroxybenzoic acid and 3,5 dihydroxy benzoic acid; quercetin and taxifolin. Linear curves concentrations ranged from 6-18 µg/mL (3,5 dihydroxy benzoic acid), 4-12 µg/mL (catechin and salicylic acid) and 2-6 µg/mL for rest of the compounds and correlation coefficients were >0.994. The limit of detection (LOD) varied from 0.04-0.45 µg/mL. Cotton root samples were used to assess the method in terms of recovery efficiency (85-120%), precision (0.12-4.09%) and intermediate precision (0.32-4.0%).Phenolics and flavonoidsin root samples of healthy and diseased plants as well as leaf samples of healthy plants were successfully quantified using this novel method without an expensive Mass Spectrometer.