Chickpea (Cicer arietinum L.) generally contains lower levels of these compounds than many other legumes, yet information on Hungarian chickpea cultivars is scarce. This study aimed to characterize protein-based antinutritional factors in twenty chickpeas grown under different agroclimatic conditions over three consecutive years (15 samples from seven Hungarian cultivars from three cultivation areas, and five commercially available foreign genotypes). Protein profiles were examined by SDS-PAGE and native PAGE, while trypsin inhibitor activity (TIA) was quantified spectrophotometrically according to ISO 14902, and lectin activity was determined using a hemagglutination assay. SDS-PAGE revealed highly similar protein patterns among samples, indicating comparable overall protein composition. Native PAGE combined with activity staining confirmed the presence of Kunitz-type trypsin inhibitors, with multiple isoforms detected, but no Bowman–Birk-type inhibitor activity was observed. TIA values were low (0.49–4.07 mg inhibited trypsin/g), and lectin activities were generally low (1–2.5 HU/mg flour; only one sample reached 5 HU/mg) or undetectable. Neither cultivation area nor growing year had a significant effect on TIA or lectin activity, confirmed by statistical analyses. Overall, Hungarian chickpea varieties exhibited low and stable levels of antinutritional proteins, supporting their favorable nutritional quality and suitability for human consumption and expanded cultivation under Hungarian agroclimatic conditions.