The Internal Standard Stable Carbon Isotope Ratio Analysis (ISCIRA) or AOAC 998.12 is a method for detecting honey adulteration using C4 sugars, such as cane and corn syrup. This method was developed and used mainly on European honeybees (Apis mellifera) and may not necessarily be applicable to honey produced by other bee species. In this study, the applicability of the ISCIRA method was validated for honeys produced by bees common to the Philippines, namely the native giant honeybees Apis breviligula, the stingless bee Tetragonula biroi, as well as Apis mellifera. Results show that authentic honeys from all three bee species collected across the Philippines (n = 14 for A. breviligula, 13 for T. biroi, and 11 for A. mellifera) displayed ISCIRA indices greater than − 1.0, validating the applicability of the ISCIRA method. Furthermore, removing suspended insoluble pollen from honey via centrifugation and filtration is not recommended as this additional step tends to shift the honey protein δ13C to a more positive value, potentially adding more leeway for C4 sugar adulteration. When the ISCIRA method was used for assessing adulteration in honey products available in the Philippine market, it was found that 12 of 16 (75%) local store-bought, 0 of 41 (0%) imported store-bought, and 64 of 74 (86.5%) local online-bought honey brands were adulterated with C4 sugars. Among the 76 adulterated honeys, 71 (93.4%) contain more than 78% apparent C4 sugar. These results demonstrate the need for stricter honey quality regulations and policies to protect the Philippines’ bee industry and its consumers.