Microorganisms are the unseen majority in soil. To better understand the effects of forest management on microbial communities, we analyzed phospholipid fatty acids (PLFAs) from litter and soil of five forest types replicated at eight sites in the framework of the Research Training Group 2300. Samples were taken between November 2017 and January 2018. Soil cores of 5 cm diameter were taken by a metal cylinder, and were separated into litter, 0-5 and 5-10 cm soil depth. In each plot three cores spaced by 5 m were taken. Samples from the same depth were pooled, resulting in 120 samples (40 plots × 3 depths). The soil was sieved through 2 mm mesh, and the litter was cut into pieces (2 mm in diameter and stones were removed. Samples were stored at -20°C. To quantify the composition of PLFAs, lipids were extracted using a modified Bligh and Dyer method. Approximately 2 g of fresh litter and 4 g of fresh soil were used for the extraction. PLFA data provide a quantitative measure of the guild abundance and community structure of microorganisms in temperate regions of Central Europe.