Quantitative chemical phenotyping is in an increasing demand to develop sweet sorghum genotypes targeted to accumulate carboxylate and polyphenolic secondary products as the plant-derived feedstocks for renewable biobased products including plastics. Of 24 sweet sorghum genotypes investigated, No. 5 Gambela (i) accumulated as much as sixfold higher (p < 0.05) trans-aconitic acid and redox-active secondary product concentrations and (ii) was most susceptible to lodging and was latest flowering. Partial least-squares calibration and prediction models were developed based on UV/visible spectra of juice and bagasse. Two-year field experiment indicated the accumulation of secondary products (carboxylates, polyphenolic chromophores, and alkali/alkaline earth metals) at the expense of fermentable sugar production. Liquid- (juice and methanol extract of bagasse) and solid-phase (bagasse without extraction) fluorescence excitation emission spectrophotometry with parallel factor analysis indicated the replacement of aromatic fingerprints by aliphatic structures from 2015 to 2016 in bagasse. In contrast, aromatic fluorophores accumulated in juice from 2015 to 2016, along with an increased UV/visible absorbance at 320 nm. Pearson's correlation analysis showed an interplay of the environmental (planting year) and genotype factors on the growth and chemical traits that could provide chemical speciation-based, bottom-up QA/QC protocols for biorefineries and chemical plants receiving the sweet sorghum bioenergy feedstock.