S. Tomé and Principe (STP) islands have been studied in recent years for their wide range of medicinal plants which exhibit several biological activities of great medicinal interest for some diseases. Experimental planning for optimization of several parameters was carried out by a full factorial of two levels of three factors for secondary metabolite extraction from Rauvolfia caffra leaves by using water and hexane at 25 and 40 ºC and 200 rpm for 0 and 5 days of incubation/extraction. The best conditions for highest extraction of phenolic compounds (i.e 89.90 moles gallic acid equivalent/g leaves)) was obtained at 25ºC, in H20 and 5 days of incubation. Several phytochemical assays were performed for characterization of these plant extracts and the highest levels of TFC, DPPH and Reducing power were obtained with aqueous plant extraction at 25ºC and for 5 days of incubation whereas leaves extraction with water at 40º C for 5 days of incubation revealed highest levels of ABTS scavenging activity. The levels of SOD and superoxide radical scavenging activities were highest with plant extraction with hexane at 25 and 40ºC for 5 days of incubation, respectively. The present report consists of a novel and intrinsic synchronous fluorescence and phosphorescence characterization of secondary metabolites from this plant extract. Intrinsic and non-destructive synchronous fluorescence was carried out in the range of 250 to 750 nm with a Δλ range of 5–30 nm which exhibited peaks at 320, 530, 550, 590, 650, 675, 690, 700, 710 nm in hexane plant extracts whereas aqueous extracts revealed only peaks at 382, 430, 460 and 530 nm. On the other hand, intrinsic and non-destructive synchronous phosphorescence was also performed which exhibited peaks at 430, 500 and 540 nm in aqueous extracts whereas hexane extracts revealed peaks at 320, 530, 560, 655, 675, 690 and 710 nm, respectively. 3-D spectra of secondary metabolites confirmed the peaks at 290, 320, 345, 400, 490 and 675 nm in plant extracts. FTIR spectroscopy was selected to investigate the structural properties of secondary metabolites in these plant extracts. Therefore, the present work describes a novel characterization of secondary metabolites by a non-destructive and intrinsic synchronous fluorescence techniques for plant extracts.