PPB carotenoids are usually measured through spectrophotometric analysis, measuring total carotenoids (TCs) which has low accuracy and cannot identify individual carotenoids or isomers. Here, we developed an ultraperformance liquid chromatography method with ultraviolet and high-resolution mass spectrometry detection (UPLC-UV-HRMS) to quantify neurosporene, lycopene, and bacteriochlorophyll a contents in PPB cultures. The method exhibited satisfactory recoveries for individual pigments (between 82.1% and 99.5%) and was applied to a range of mixed PPB cultures. The use of a C 30 column also enabled the detection of three different isomers of lycopene. In addition, a method for anaerobic photoheterotrophic PPB cultivation to acquire live-cell spectrophotometric information was developed and tested by modifying a standard microbial culture microplate system. A rapid, and relatively low effort principal component analysis (PCA) based decomposition of the whole-cell spectra for pigment analysis in the microplates was also developed. Analysing whole-cell spectra via PCA allowed more accurate prediction of individual pigments compared to absorption methods, and can be done nondestructively, during live-cell growth, but requires calibration for new media and microbial matrices.