Cover crops provide many agroecosystem services, including weed suppression, which is partially exerted through release of allelopathic benzoxazinoid (BX) compounds. This research (1) characterizes changes in concentrations of BX compounds in shoots, roots, and soil at three growth stages (GS) of cereal rye (Secale cereale L.), and (2) their degradation in soil over time following termination. Concentrations of shoot dominant BX compounds, DIBOA-glc and DIBOA were lowest at GS 83 (boot). The root dominant BX compound, HMBOA-glc, concentration was least at GS 54 (elongation). Rhizosphere soil BX concentrations were 1000 times smaller than in root tissues. Dominant compounds in soil were HMBOA-glc and HMBOA. Soil BX compound concentrations were similar near root crowns and between-rows. Soil BX concentrations following cereal rye termination declined exponentially over time in three of four treatments: incorporated shoots (S) and roots (R), no-till S + R (cereal rye rolled flat), and no-till R (shoots removed); no-till S had consistently low concentrations. In treatments showing changes, soil concentrations of HMBOA-glc and HMBOA increased above initial concentrations on the day following cereal rye termination. Concentrations of these two compounds decreased more rapidly than the other compounds. Placement of shoots on the surface of an area where cereal rye had not grown (no-till S) did not increase soil concentrations of BX compounds. The short duration and complex dynamics of BX compounds in soil prior to and following termination illustrate the limited window for enhancing weed suppression directly by cereal rye allelochemicals; valuable information for programs breeding for enhanced weed suppression.