Measuring the degree of organic matter (OM) alteration caused by uranium (U) irradiation is important in the effective evaluation of the hydrocarbon potential and thermal maturity of U-rich source rocks. This study investigates OM alteration in the Baltoscandian U-rich, lower Paleozoic Alum shale obtained from three research wells in the thermally immature parts of eastern Sweden and western Estonia. The results show a marked increase in the proportion of refractory, non-generative organic carbon (NGOC) in the U-rich shale. Fluorescence spectrometry of unicellular alginites and lamalginites show a reduction of up to 95.6% in fluorescence relative intensity (RI) with increase in U content from 29 to 401 ppm. Fluorescence spectra of the liptinites exhibit a marked “red shift” as expressed by increase in red(R)/green(G) quotients. This change in fluorescence properties of the liptinites is associated with up to 77.6% decrease in hydrogen index (HI) and hence loss of hydrocarbon generation potential. Furthermore, organic molecules show significant loss of aromatic moieties as well as aliphatic constituents resulting in a more condensed macromolecular structure. The measured random reflectance of solid bitumen (BRo) appears to be significantly elevated in micro scale proximity to the U-containing minerals. The heterogeneous distribution of U-containing minerals and the contact with solid bitumen attributes to the wider range of BRo values and lead to the overall increase in mean BRo in samples with high U contents. In contrast, Ro values of zooclast macerals (GRo, e.g., graptolite, chitinozoans and vitrinite-like fragments) appear to be less influenced by U irradiation and hence are a more reliable maturity indicator in U- rich lower Paleozoic shales.