The impact of four different harvest years and two cultivation locations (CLs) of pea seeds on their protein wet fractionation yield, volatile and non-volatile beany flavors, and functionality were investigated. Both harvest years and CLs significantly affected protein recovery, but protein purity was primarily influenced by CLs. Seed age emerged as a dominant factor causing the reduction in linolenic/linoleic acid content and lipoxygenase (LOX) activity which surpassed the effect of harvest years in the seeds but not in their proteins. CL significantly affected fatty acid composition in both seeds and proteins, whereas its effect on LOX activity was discernible only in the proteins. Volatile beany compounds in the proteins were affected by both harvest years and CLs, correlating with their polyunsaturated fatty acid (PUFA) content and LOX activity. Both factors minimally impacted the emulsification capacity of the proteins but imposed a significant effect on their rheological properties. Altogether, the results revealed that seed crop years and especially locations affect pea protein quality, calling for proper adaptation strategies.