Growing cereals (especially rye), which are incorporated into the soil to increase soil fertility or organic matter content, is a common practice in crop rotation. The additional sanitizing effect of this incorporation has often been appreciated and is said to be due to leaching of benzoxazinones and subsequent formation of benzoxazolinones. In this study wheat (Stakado) and rye (Hacada) sprouts were incorporated into soil in amounts that simulated agricultural practice. By extraction and subsequent LC-MS analysis the disappearance and appearance of benzoxazinones, benzoxazolinones, and phenoxazinones in soil were followed. In the wheat experiments 6-methoxybenzoxazolin-2-one (MBOA) was detected as the main compound. 2-Hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA) and 2-hydroxy-1,4-benzoxazin-3-one (HBOA) were detected as well. No phenoxazinones were detected. For the rye experiment the picture was more complex. In the first 2 days of incubation MBOA and 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) were detected as the main allelochemicals along with HBOA, HMBOA, and benzoxazolin-2-one (BOA), in decreasing order. Later in the incubation period some 2-amino-3H-phenoxazin-3-one (APO) was detected and the amount of HBOA increased considerably and decreased again. The profiling of the benzoxazinone metabolites and their derivates in soil was dynamic and time-dependent. The highest concentrations of most of the compounds were seen at day 1 after incorporation. A maximum concentration was reached at day 4 for a few of the compounds. This study is the first of its kind that shows the dynamic pattern of biologically active benzoxazinone derivates in soil after incorporation of wheat and rye sprouts. Methods for organic synthesis of HBOA and HMBOA were developed as part of the study.