Manure contains several compounds that can potentially cause foaming during anaerobic digestion. Understanding the effect of substrates and intermediate compounds on foaming tendency and stability could facilitate strategies for foaming prevention and recovery of the process. In this study, the effect of physicochemical properties of substrates and intermediate compounds on liquid properties such as surface tension, surfactant property, and hydrophobicity were investigated and compared with the effect on foaming tendency and foam stability. The results showed that there was no consistent correlation between foaming potential and hydrophobicity, oil displacement area (ODA) or surface tension of the tested solutions, and the best way to determine the foaming property of the solution was to directly measure foaming tendency and foam stability. Na-oleate and acetic acid showed the highest potential to create foam in a manure digester. Moreover, high organic loading of lipids and protein, and high concentrations of acetic and butyric acids also showed a strong tendency to create foaming during anaerobic digestion. Due to their great ability to stabilize foam, high organic loadings of Na-oleate or gelatine were considered to be the main potential foaming problem.