The zinc finger transcription factor STOP1 plays a crucial role in aluminum (Al) resistance and low phosphate (Pi) response. Al stress and low Pi availability do not affect mRNA expression but are able to induce STOP1 protein accumulation by post-transcriptional regulatory mechanisms. We recently reported that STOP1 can be mono-SUMOylated at K40, K212, or K395 sites, and deSUMOylated by the SUMO protease ESD4. SUMOylation of STOP1 is important for the regulation of STOP1 protein function and Al resistance. In the present study, we further characterized the role of the SUMO E3 ligase SIZ1 in STOP1 SUMOylation, Al resistance and low Pi response. We found that mutation of reduced but not eliminated STOP1 SUMOylation, suggesting that SIZ1-dependent and -independent pathways are involved in the regulation of STOP1 SUMOylation. The STOP1 protein levels were decreased in mutants. Nevertheless, the expression of STOP1-target gene was increased instead of reduced in mutants. The mutants showed enhanced Al resistance and low Pi response. Our results suggest that SIZ1 regulates Al resistance and low Pi response likely through the modulation of expression.