The aim of the present study is focused on the decolorization and degradation of azo dyes Ponceau S Red and Methyl Orange by a bacterial strain isolated from the gold mining district of San Martin de Loba, South of Bolivar (Colombia) sediment samples and identified as Franconibacter sp. 1MS (GenBank: MT568543) based on phenotypic and genotypic methods. A higher percentage of decolorization at 100 mg/L concentration, 37 °C, and pH 7 was recorded at 120 h of incubation period for both dyes. The UV–vis, Fourier transform infrared spectroscopy, and gas chromatography–mass spectrometry analysis of the original dyes and their degraded metabolites confirmed that the decolorization was due to degradation. The proposed metabolic pathways for biodegradation of both dyes have been elucidated, which showed the formation of five intermediate metabolites, namely, N,N-dimethylbenzyl-1,4-diamine, sulfonamide, 1,4-diaminobenzene, 2,5-diaminobenzenesulfonic acid, and 1-amino-2-naphthol, which are not only highly toxic but also be able to be converted through metabolic activation into mutagenic, carcinogenic, and/or teratogenic species. The phytotoxicity studies of the original dye and degraded metabolites were tested on Phaseolus vulgaris and divulged that the degraded metabolites have toxic effects. An effective phytostimulation was observed in Ponceau S Red, which could be attributed to its capacity for enrichment of the culture medium with essential nutrients, a favorable environment for the growth of the plant.