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Phytic acid (PA) acts as an antinutrient substance in cereal grains, disturbing the bioavailability of micronutrients, such as iron and zinc, in humans, causing malnutrition. <i>GmIPK1</i> encodes the inositol 1,3,4,5,6-penta<i>kis</i>phosphate 2-kinase enzyme, which converts <i>myo</i>-inopsitol-1,3,4,5,6-penta<i>kis</i>phosphate (IP₅) to <i>myo</i>-inositol-1,2,3,4,5,6-hexakisphosphate (IP₆) in soybean (<i>Glycine max</i> L.). In this study, for developing soybean with low PA levels, we attempted to edit the <i>GmIPK1 <i>gene</i></i> using the CRISPR/<i>Cas9</i> system to <i>introduce</i> mutations into the <i>GmIPK1</i> gene with guide RNAs in soybean (cv. Kwangankong). The <i>GmIPK1</i> gene was disrupted using the CRISPR/Cas9 system, with sgRNA-1 and sgRNA-4 targeting the second and third exon, respectively. Several soybean <i>Gmipk1</i> gene-edited lines were obtained in the T₀ generation at editing frequencies of 0.1–84.3%. Sequencing analysis revealed various indel patterns with the deletion of 1–9 nucleotides and insertions of 1 nucleotide in several soybean lines (T₀). Finally, we confirmed two sgRNA-4 <i>Gmipk1</i> gene-edited homozygote soybean T₁ plants (line #21-2: 5 bp deletion; line #21-3: 1 bp insertion) by PPT leaf coating assay and PCR analysis. Analysis of soybean <i>Gmipk1</i> gene-edited lines indicated a reduction in PA content in soybean T₂ seeds but did not show any defects in plant growth and seed development.