Maesa indica Roxb. Sweet is a shrub known for its richness in secondary metabolites. A callus culture protocol was established to enhance its chemical profile. Sixteen elicitation culture treatments were evaluated, and we confirmed that the treatment of 200 mg/L polyethylene glycol (4000) coupled with exposure to 30 W UV irradiation for 60 min (PEG4) resulted in the highest total phenolic and total flavonoid contents, which were 4.1 and 4.9 times those of the plant ethanolic extract and 4.9 and 4.8 times those of a control sample, respectively. The phenolic compounds in the different treatments were identified qualitatively and quantitatively using the LC-ESI-MS/MS-MRM technique. Molecular docking studies of the phenolic compounds were conducted using MOE software and revealed that rutin showed the highest binding affinity toward the anti-cancer target (p38α MAPK). The cytotoxicity of the ME and PEG 4 treatment was tested against colon, breast, prostate, lung, and liver cell lines using an MTT assay. The highest cytotoxic effect of PEG4 was against prostate cancer with an IC50 value of 25.5 µg/mL. Hence, this study showed enhanced secondary metabolite accumulation and identified the phenolic compounds in the 16 treatments. The cytotoxicity assay highlighted the possible cytotoxic effect of the PEG4 treatment, and we recommend further investigations into its activity.