Propolis is a complex biological matrix whose composition consists mostly of plant resins and waxes, and in a small fraction of herbal secondary metabolites, phenols. Phenols are responsible for a wide range of positive effects on human health and are used as active components in various medical products as extracts. However, selection of an extraction method that would provide high yield of phenolic components, but would also be safe for human use, remains a big challenge. Therefore, various water- and oil-based propolis extracts were analyzed herein. Optimal conditions for isolation of each of the phenols in the extracts were determined by chemometric data processing. In the process of development and manufacturing of propolis-based products, selection of appropriate raw materials and standardization of the final products are crucial elements. This can be secured only upon complete characterization of the initial raw material. For this purpose, selective and non-selective analysis of propolis extracts on mass spectrometry-based instruments were developed. For quantitative analysis, liquid chromatography coupled to triple quadrupole (LC-QQQ) was used, whereas for qualitative non-selective profiling, direct flow injection electrospray coupled to quadrupole time-of-flight (ESI-QTOF) and liquid chromatography coupled to QTOF (LC-QTOF) were employed. A total of 56 samples of propolis from the Republic of Croatia were qualitatively and quantitatively analyzed. The results showed that, contrary to expectations, the European poplar type is not the only type of propolis in the Republic of Croatia. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) have shown that the poplar type overlaps with the Mediterranean type on the Croatian coast, especially on the islands. For quick determination of the type of propolis, ESI-QTOF method was a method of choice, while LC-QTOF method was a method of choice for total profiling and identification of phenolic components specific for Croatian propolis and components specific for each Croatian region. At last, the most successful water- and oil-based extraction procedures were selected, and extracts of the two types of propolis were prepared using these procedures. The results point to significant differences in the phenolic fractions of the obtained extracts. This research showed that propolis samples from the Republic of Croatia substantially differ in the phenolic composition which pinpoints the importance of appropriate extraction method development with respect to the wanted extract compisition and biological effect. Taken as a whole, this study represents a contribution towards resolving the problem of standardization of propolis-based products.