[Aim] The present study assessed the effects of agrochemicals on indigenous citrus endophytes. [Method] The compatibility of six pesticides, three bactericides, and one micro-element fertilizer with the endophytic strain Bacillus subtilis L1-21 was tested. [Result] Citrus endophyte suppression ability was monitored through population dynamics on plates and after spraying on citrus leaves. The results suggested that 56.00 mg·L^-1 imidacloprid, 121.80 mg·L^-1 chlorfenapyr, 4.00 mg·L^-1 methylaminoabamectin, 50.00 mg·L^-1 thiamethoxam, 45.60 mg·L^-1 cyfluthrim, 800.00 mg·L^-1 phoxim, 402.00 mg·L^-1 oxine-copper, 3728.00 mg·L^-1 sulphur, 620.60 mg·L^-1 cuprous oxide, and 321.00 mg·L^-1 EDTA-Cu completely suppressed the endophyte L1-21 growth on plates . The 2-fold treatment on detached leaves after 24 h suggested an inhibition rate of methylaminoabamectin 8.00 mg·L^-1 (16.84%) that was significantly lower than the five pesticides tested. However, no significant difference was found in the inhibition rate by these five pesticides on endophyte L1-21. In vivo results showed that the inhibition rate caused by 8.00 mg·L^-1 of methylaminoabamectin on L1-21 inside citrus leaves (4.23%) was not serious, and lower than the ones caused by the five pesticides, three bactericides and micro-element EDTA-Cu. The lowest inhibition rate on citrus endophytes was recorded for 8.00 mg·L^-1 methylamino-abamectin (6.78%), and it was 46.90%-70.06% for other agrochemicals with no significant difference among them. [Conclusion] The ten examined agrochemicals can inhibit endophyte L1-21 on plates in a concentration-dependent manner. In addition, these agrochemicals directly affect endophyte L1-21 in citrus leaves, resulting in a reduced number of endophytes, and the adverse effect of these agrochemicals on citrus endophytes cannot be neglected.