This article presents the results of spectroscopic studies of two compounds from the 1,3,4-thiadiazole group, that is, 4-(5-methyl-1,3,4-thiadiazole-2-yl)benzene-1,3-diol (C1) and 4-(5-heptyl-1,3,4-thiadiazole-2-yl)benzene-1,3-diol (C7), present at different molar concentrations in 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) liposome systems. In the case of both investigated compounds, fluorescence measurements revealed the presence of several emission bands, whose appearance is related to the molecular organization induced by changes in the phase transition in DPPC. On the basis of the interpretation of Fourier transform infrared spectra, we determined the molecular organization of the analyzed compounds in multilayers formed from DPPC and the 1,3,4-thiadiazoles. It was found that the compound with a longer alkyl substituent both occupied the lipid polar head region in the lipid multilayer and interacted with lipid hydrocarbon chains. In turn, the compound with a shorter alkyl substituent interacted more strongly with the membrane polar region. On the basis of the knowledge from previous investigations conducted using different solvents, the fluorescence effects observed were related to the phenomenon of molecular aggregation. The effects were strongly influenced by the structure of the compound and, primarily, by the type of the alkyl substituent used in the molecule. The substantial shortening of fluorescence lifetimes associated with the effect of long-wave emission (with a maximum at 505 nm) decay also confirms the model of aggregation effects in the analyzed systems. Similar effects can be very easily distinguished and associated with respective forms of the compounds in biologically relevant samples.