To explore the effects of different preservation methods on the quality of loquat after fresh-keeping treatment, various preservation techniques were employed. These included natural preservation (NP), vacuum freezing preservation (VFP), vacuum at room temperature preservation (VP) and freezing preservation (FP). The quality assessment involved analyzing the effects of these preservation methods using physicochemical indexes, a colorimeter, an electronic nose (E-nose), an electronic tongue (E-tongue) and gas chromatography–mass spectrometry (GC–MS). The results showed minor differences in loquat quality under different preservation methods, with sensory scores ranging from 55 to 78 and ΔE values ranging from 11.92 to 18.59. Significant variations were observed in moisture content (ranging from 53.20 g/100 g to 87.20 g/100 g), calorie content (ranging from 42.55 Kcal/100 g to 87.30 Kcal/100 g), adhesion (ranging from 0.92 to 1.84 mJ) and hardness (ranging from 2.97 to 4.19 N) (p < 0.05). Additionally, the free amino acid content varied from 22.47 mg/g to 65.42 mg/g. GC–MS analysis identified a total of 47 volatile flavor substances in varieties of loquats, including 13 aldehydes, 9 esters, 6 ketones, 2 acids, 3 alcohols, 2 phenols, 3 pyrazines, 1 furan and 8 other substances. The relative content of aldehydes was significantly higher than that of other chemicals. The VFP and FP samples exhibited higher aldehyde content compared to the NP and VP samples. Moreover, Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) revealed 18 marked compounds that could differentiate between 5 loquat species. Analysis using E-nose and E-tongue indicated significant changes in the olfactory and gustatory senses of loquats following preservation. The VFP samples demonstrated the most effective preservation of loquat quality with minimal impact. This study provides some theoretical guidance for the home preservation of loquats.