AbstractPennycress (Thlaspi arvense L.) is a winter oilseed crop that also functions as cover crop, oil feedstock for biofuel, and novel plant‐based protein. New pennycress specialty varieties were developed by conventional breeding techniques, but protein chemical and functional traits are still unknown. This research evaluated three new lines (black‐seeded B3 and yellow‐seeded TTG1/Y1126 and TT8) for protein extractability and functionality. Seeds were ground cryogenically and then hexane‐defatted until residual oil content was 0.5%–0.7% dry basis, db. Protein in defatted seed meals was extracted using saline method (1: 10 wt/vol, 0.1 M NaCl, 2 h, 50°C). TT8 and Y1126 had greater protein recoveries (ca. 50%) than those of B3 (36%) and wild‐type pennycress (WTP, 40%). TT8 produced higher purity protein isolate (94.3%) than did Y1126 (75.0%) and B3 (71.3%). TT8 and Y1126 protein band patterns were different from WTP and B3, reflecting varietal changes. The new varieties' protein extracts were more soluble than WTP protein in acidic pH, with TT8 showing the highest solubility (81%–93%). TT8, Y1126 and B3 foaming capacities (113–135 ml) were superior to those of WTP (101–107 ml). Emulsification properties (EAI 95–230 m2/g protein, ESI 13–24 min) were similar and increased with pH. B3, Y1126, and TT8 formed heat‐induced gels at much lower concentration than did WTP (3% vs. 6%) and their water‐holding capacities (pH 7) were two to fivefold greater. This work demonstrated that mutations in the TTG1 or TT8 gene in yellow‐seeded lines resulted in improved protein recoveries and functionalities that are desirable in plant‐based proteins.