This is the first report to identify the presence of 3-O-caffeoyl quinic acid (1), 4-O-caffeoyl quinic acid (2), 5-O-caffeoyl quinic acid (3), epi-catechin (4), and procyanidin B2 (5) in the young propagules of Rhizophora mucronata. Compounds 2–5 were purified and then treated against breast, colorectal, and ovarian cancer cell lines for 72 h and the results of the Sulphorhodomine-B (SRB) assay were evaluated for percent cell viability and IC₅₀ values. Epi-catechin, 4-O-caffeoyl quinic acid, 5-O-caffeoyl quinic acid and procyanidin B2 showed strong to moderate inhibitory effects when treated on breast (T47D), colorectal (HT29), and ovarian (A2780, SKOV3) cancer cell lines with IC₅₀ values ranging from 16.77 ± 0.58 to 28.28 ± 0.89 μg/mL. In silico evaluation was performed to evaluate the drug-likeness and toxicological effects of these compounds using Molinspiration calculation and OSIRIS program. It was found that compounds 2, 3, and 4 have the potential to be orally active and have a low risk in exerting the mutagenic, tumorigenic, irritant, and reproductive effects.