This study involved comparison of different extraction and derivatization methods for determining FAs in soil and in four highly organic matrixes (cattle manure, pig slurry, compost, and vermicompost), by application of a multifactor categorical design. Although some studies have been carried out regarding the application of FA analysis to highly organic matrixes, comparison and verification are still required to test which methods of extraction and derivatization of FAs function best for these matrixes. We compared three extraction methods (one in which the same extraction mixture as used in the Folch method was employed, a modification of the Bligh and Dyer method, and a microwave-assisted extraction) and two derivatization procedures (alkaline methanolysis and derivatization with trimethylsulfonium hydroxide (TMSH)). The highest yields of FAs belonging to different structural classes, and of individual FAs used as microbial biomarkers were obtained by application of the same extraction mixture as in the Folch method and use of TMSH as derivatization agent. These methods also involved a significant reduction in the complexity and time involved in sample preparation.