An identified reference germplasm is needed to facilitate the stable sourcing of medicinal plants with correct genotype(s). We aimed to evaluate phytochemical and agro-morphological properties of four pre-selected, genetically stable, and native Vitex trifolia s.l. accessions from the Philippines to provide baseline information and present promising and available genetic materials as standards. Yield and yield components of four V. trifolia s.l. accessions from the Philippine Biorepository Network (PBN) were evaluated using a randomized complete block design in one growing season. Quantification of macromolecules of the dried samples were determined through proximate analysis. Phytochemicals were qualitatively screened while antioxidant activity were evaluated for total phenolic content, DPPH radical scavenging activity, and hydrogen peroxide scavenging activity. PBN 2019–138 had the highest dry yield at 128 ± 21.16 g per plant and showed moderate to high antioxidant activity. Its high biomass throughput was attributed to its higher number of leaves per plant, heavier petiole weight, and high fiber content at 25.29%. PBN 2019–332 exhibited the highest antioxidant activity among all assays but with relatively lower fiber content (24.24%) and lower yield at 60.62 ± 17.63 g per plant. The genotypes varied significantly in 17 out of 29 evaluation parameters. Thirteen traits had moderate to high heritability values, indicating the potential for clonal selection of promising types. Using principal component analysis, we identified PBN 2019–138 as the most promising genotype across the four accessions as it had the highest leaf yield per plant and intermediate antioxidant activity. Thus, the accessions presented can be asexually propagated and used as genotypic standards for subsequent RDE activities centered on the medicinal use of V. trifolia s.l. genotypes.