Green solvents are being used to replace the conventional organic solvents in combination with green technologies. In this context, Peruvian Pouteria caimito fruit was used as a model for our study. The main objective was to explore an environmentally friendly strategy for the extraction of phenolics, by microwave or maceration using ethyl lactate and methanol as extraction solvents. Thus, each extract was compared by liquid chromatography coupled to tandem mass spectrometry (LC-ESI-MS/MS) to propose an alternative for the extraction processes and their antioxidant activity. The results showed that the two extraction methods had effects on the extraction yields, with microwave-assisted extraction (17.5% in MeOH and 8.0% in ethyl lactate) proving to be a better method for extracting the phenolic compounds than maceration extraction (12.2% in MeOH and 4.3% in ethyl lactate). In the case of LC/ESI/MS/MS studies the same trend was detected. Microwave extraction detected the presence of twenty-three compounds mainly including dicaffeoylquinic acid, monocaffeoyl quinic acids, feruloylquinic acids, galloylquinic acid, protocatechuic acid hexoside, ferulic acid and quercetin; while on maceration extraction between 15 up to 17 metabolites were identified. In this sense, microwave-assisted extraction was more efficient than maceration in terms of the number of metabolites extracted. The quantitative analysis of quercetin by high-performance liquid chromatography (HPLC) of all extracts showed no significant differences (around 8.704 up to 8.707 ± 0.019 mg/g extract). Finally, the antioxidant activity, in terms of ORAC (oxygen radical absorbance capacity) was higher in extracts prepared by microwave (93.51–97.05 mg TE/g extract) than in those prepared by maceration (77.25–86.88 mg TE/g extract). In the case of DPPH (2,2-diphenyl-1-picrylhydrazyl), the antioxidant activity was higher in extracts prepared by microwave (IC50: 50.40–53.80 μg/mL) than in those prepared by maceration (IC50: 67.6–74.10 μg/mL). Therefore, based on our results, a green extraction technique such as microwave-assisted extraction, compared to maceration, is faster, greener, and more sustainable alternative and could replace classical extraction techniques reducing negative side effects for both the environment and the analyst. These findings could be seen as a great potential for industrial and pharmaceutical processes to reduce the negative impact of using toxic organic solvents.