Seeds are an important part of plants, ensuring the continuation of plants’ life and providing nutrient reserves for humans and animals. Seed development is controlled by the interplay of several physiological processes. We applied label-free proteomics to round and wrinkled peas using seeds sampled at five growth stages (4 days after anthesis (DAA), 7DAA, 12DAA, 15DAA, and maturity). Phenotypic results indicated that wrinkled peas had lower starch concentration compared to round peas (29.5% vs. 46.6-55.1%). A total of 4,126 high confident proteins were detected, with 22–26% shared across all sampling times within an entry. Early seed growth stages were characterized by more unique proteins compared to maturity. Two-way ANOVA revealed 1,685 proteins significantly different among samples, of which 722 proteins were characterized into 29 functional classes. The four major classes (comprising over 50 proteins) were protein biosynthesis, protein homeostasis, enzymes, and carbohydrate metabolism. Of the two types of comparisons (time-point and entry-wise), time-point comparisons yielded more differentially abundance proteins (596 proteins in total). Different protein classes exhibited different patterns of change during seed development. For example, cell division related proteins were abundant early in seed development, whereas storage proteins were abundant later in seed development (especially after 12DAA). Compared to the round pea entries, the wrinkled entry had significantly lower abundance of starch branching enzymes, a protein involved in the biosynthesis of amylopectin in starch. In conclusion, the results of this study provide valuable information to improve our understanding of seed development and form the basis for further studies.