This study addresses the methodological and ecological challenges of evaluating soil legacy and allelopathic residual effects in agroecosystems. The allelopathic activity of edaphotopes from five agroecosystems (fallow with mixed herbage, apricot, walnut, Echinacea purpurea and an abiotic sand control) was evaluated with 16 test crops in a three-level hierarchy: 8000 seeds, 320 trays and 80 crop-by-agroecosystem cells. Because the soil of each agroecosystem was collected as a single composite sample, the four trays are technical subsamples; inference on the agroecosystem factor was therefore drawn at the crop-block level, with the 16 test crops acting as independent bioassays of the same soils. Morphometric measurements were modelled with binomial generalized linear mixed models for germination and viability and with linear mixed models of log-transformed root length, shoot length and their ratio, and were summarised by the Normalized Response Index, the Stress Effect Index and a Composite Vigor index. After correction for multiple comparisons across all ten pairwise contrasts, one difference between agroecosystems was supported: fallow with mixed herbage exceeded the Echinacea purpurea soil in Composite Vigor (Δ = 1.440; 95 % CI 0.572 to 2.308; p[Holm] = 0.030), with the same contrast supported for root length, shoot length and the Normalized Response Index; germination, viability and the Stress Effect Index showed no differences at this level. The response was strongly crop-specific: Kendall's coefficient of concordance across the 16 crops was 0.170, so the ranking of agroecosystems obtained with one test species is largely not transferable to another. Variance partitioning attributed 43.3% to 91.8% of the variation to the biology of the test crop and at most 7.4% to the agroecosystem, with 23.1% of the variation of Composite Vigor residing in the crop-by-agroecosystem interaction. In the multivariate analysis at the replicate level the test crop accounted for 70.7 % of the variation, the interaction for 16.7% and the agroecosystem for 3.1% (PERMANOVA, 9999 permutations). The study demonstrates that a multi-level mixed modelling framework with explicit attention to the level of replication yields a defensible, if narrower, description of the soil allelopathic regime, and that bioassays based on a single test species are not a reliable instrument for ranking agroecosystems.