Food contact materials (FCM) may contain complex mixtures of estrogenic chemicals. A yeast estrogen screen performed on high performance thin-layer chromatography plates (planar-YES, P-YES) is promising for analysis of such mixtures, as it could allow for better elucidation of effects compared with established methods in microtiter plates. However, the P-YES has not been directly compared with established methods. We compared the performance of a microtiter plate YES (lyticase-YES, L-YES) to P-YES on silica gel HPTLC plates using 17β-estradiol (E2), 20 chemicals representative of migrants from plastic FCM, and three migrates of coated metal food cans. Effective doses (ED10, ED50) and estradiol equivalencies were calculated for each chemical. Thirteen chemicals had calculable EDs in the L-YES or P-YES, with average EDs 13-fold (range 0.63–36) more potent in P-YES than in the L-YES. Normalized to E2, the median estrogenicity was within 1.5-fold (0.43–8.8) between the assays. Therefore, P-YES was as or more sensitive than L-YES but potencies relative to E2 were comparable between assays. With chromatography, the P-YES detected estrogenicity in coated metal cans, effects that were unmeasurable in L-YES. With the sample preparation methods used in this study, both YES assays are sufficiently sensitive to detect bisphenol A below the specific migration limit for plastic packaging (0.05 mg/kg food). This study demonstrates that P-YES outperforms L-YES because it is more sensitive, provides comparable estradiol equivalents, and circumvents confounding mixture effects. The P-YES will be useful for routine monitoring of FCM and toxicant identification in problematic materials.