Objective Stem cells of human exfoliated deciduous teeth (SHED) metabolites are secreted molecules from SHED, namely cytokines, chemokines, and growth factors. The metabolite can be used in various regenerative therapy based on cell-free immunomodulatory potential effects, like interleukin 10 (IL-10) and LL37. This molecule can stimulate with epigallocatechin gallate (EGCG) and α-mangosteen and has been proven to have anti-inflammatory and antibacterial effects. This study aimed to identify the effect of EGCG and α-mangosteen to SHED metabolite, called SHED-IL10 and SHED-LL37, from six passages to obtain the optimum stimulation and able to use as periodontitis regeneration treatment. Materials and Methods The six different passages of SHED were prepared in Dulbecco's modified Eagle medium and added with EGCG 80% (10 μM), EGCG 95% (10 μM), or α-mangosteen (10 μM). After a 24 hours incubation, each passage was measured with the metabolite concentration, SHED-IL10 and SHED-LL37, with human IL-10 and LL37 using enzyme-linked immunosorbent assay. Each different concentration was then analyzed statistically. Results The addition of EGCG 95% is able to stimulate the SHED-IL10 optimum concentration in passage 1 (p < 0.01). But, in the different conditions, the addition of EGCG 80%, EGCG 95%, and α-mangosteen was able to stimulate the SHED-LL37 optimum concentration in passage 2 (p < 0.001). Conclusion The addition of EGCG and α-mangosteen can stimulate the SHED-IL10 and SHED-LL37 concentrations. These two metabolites are promising as regenerative therapy through anti-inflammatory and antibacterial properties.