On the basis of earlier results with furan and thiophene derivatives of benzobicyclo[3.2.1]octadiene, photocatalytic oxygenation of novel furo- and thieno heterostilbenes with water-soluble manganese(III) porphyrins offered suitable possibilities to study their reactivities and reaction pathways depending on the heteroatom and the catalyst charge. The experiments were carried out in two reactors types (batch and microflow) to investigate the geometric effects. NMR spectroscopy, GC, and UPLC/MS analyses were applied for identification and quantification of the products. As our results indicated, the 2-thienyl and the common p-tolyl groups in the starting compounds remained intact due to their stronger aromaticity. Hence, the thieno derivative underwent oxygenation only at the open-chain part of the molecule, and the rates of its reactions were much lower than those of the furyl analogue. The less stable furan ring was easily oxygenated, its products with highest ratios were 2-furanon derivatives. Epoxide formation occurred at the open-chain parts of both substrates preferably by the anionic catalyst. Nevertheless, the conversion rates of the substrates were higher with the cationic porphyrin, according to electrophilic attacks by photogenerated Mn(V)=O species. Additionally, the reactions were significantly faster in microflow reactors due to the more favorable circumstances of mass transfer, diffusion, and light penetration.