Pectin is a natural polymer that is found in the cell walls of higher plants. This study presents a comprehensive analysis of pectin extracted from lemon in two different geographic regions (Peddie and Fort Beaufort) in two consecutive years (2023 and 2024) named PP 2023, PP 2024, FBP 2023, and FBP 2024. The dried lemon peels were ground into a powder, sifted to obtain particles of 500 μm, and then subjected to pectin extraction using a conventional method involving mixing lemon peel powder with distilled water, adjusting the pH level to 2.0 with HCl, heating the mixture at 70 °C for 45 min, filtering the acidic extract, and precipitating pectin with ethanol. The yield of these pectin samples was statistically significant, as FBP 2024 had a maximum yield of 12.2 ± 0.02%, PP 2024 had a maximum yield of 13.0 ± 0.02%, FBP 2023 had a maximum yield of 12.2 ± 0.03%, and PP 2023 had a maximum yield of 13.1 ± 0.03%, The variation in yield could be due to the differences in the growing conditions, such as the climate and soil, which could have affected the pectin content in the lemons. The physicochemical characterization of all samples proved that our pectin samples could be used in the pharmaceutical and food industries, with anhydrouronic acid content which was greater than 65%, as suggested by the FAO. The scanning electron microscope analysis of all extracted pectin was rough and jagged, while the commercial pectin displayed a smooth surface morphology with a consistent size. FTIR confirmed the functional groups which were present in our samples. Thermogravimetric analysis was employed to investigate the thermal behavior of the extracted pectin in comparison with commercial pectin. It was found that the extracted pectin had three-step degradation while the commercial pectin had four-step degradation. Additionally, pectin samples have been shown to have antioxidants, as the IC50 of PP 2024, PP 2023, FBP 2023, FBP 2024, and Commercial P was 1062.5 ± 20.0, 1201.3 ± 22.0, 1304.6 ± 19.0, 1382.6 ± 29.9, and 1019.4 ± 17.1 mg/L, respectively. These findings indicate that lemon pectin has promising characteristics as a biopolymer for use in biomedical applications.