This paper reports a study on analyte/matrix effects of multicomponent FL mixtures of lumichrome (1), 3-methyl-lumiflavin (2), riboflavin (3) in the presence of uric acid (4), redox-stabilizers such as resorufin (5), resazurin (6) and naturally plant originating food color additive maclurin (7), respectively. Sampling complexity, in particular the spatial distribution of the experimental parameters, which can vary widely, is a critical challenge for achieving the selectivity for application to the environmental and foodstuff assays. The random distribution of the analyte in a real sample as well as the systematic and random errors at each of the analytical steps alter the variables of interest. The samples are very complex regarding the nature and matrix effects; significantly alert the recovery, than the choice of an instrumental method for determination, is the most important step. This paper places emphasis on UV-MALDI-Orbitrap-MS among the irreplaceable robust mass spectrometric methods. Despite its conceptually different quantitation procedure from the HPLC-ESI(or APCI)-MS ones, the method provided accurate and precise analytical information over a large concentration range up to 100 fg μL−1, high resolution power and screening ability of individual molecules in complex mixtures, solution, semi-liquid and solid-state analysis, short assay time, fast and step-limited sample pretreatment stages. The reported protocol is constructed on real analytical problems as an effective approach, ensuring maximal data representativeness towards the matrix effects typical for FL assay (pH scale ∈ 2.0–11.8, solvent polarity e ∈ 7.5–80.1, solvent donor number DN ∈ 14.1–31.5 kcal mol−1, T ∈ 25–300 °C), because of 1–7 stabilized different tautomeric forms, redox states and hydrogen bonding networks. The content included: (a) experimental and theoretical MS analyses and factors stabilizing the ionic fragments in the GP, determining the intensity; (b) full validated (methods and techniques) ESI-, APCI- and MALDI-MS protocols; (c) comparative analysis, employing EAs, LC, HPLC, and UHPLC methods and (d) chemometrics. The promising metrology achieved, beyond that of the reported UPLC-MS/MS, MW-HPLC, and UHPLC ones, evidenced the great capability of the UV-MALDI-Orbitrap-MS method for environmental and foodstuff monitoring versus the widely implemented microbial, chromatographic and spectrometric methods.