Phytate-phosphorus (P) in food and feed is not efficiently utilized by humans and non-ruminant livestock, potentially contributing to high losses of P to the environment. Crops with high P-acquisition efficiency can access soil P effectively. It remains elusive whether crop genotypes with high P-acquisition efficiency can also have low seed phytate concentrations. A core collection of 256 soybean [Glycine max (L.) Merr.] genotypes from China with diverse genetic background were grown in the same environment and seeds were sampled to screen for seed phytate-P concentration. Some of these genotypes were also grown in a low-P soil in the glasshouse to measure root morphological and physiological traits related to P acquisition. Large genotypic variation was found in seed phytate-P concentration (0.69–5.49 mg P g–1 dry weight), total root length, root surface area, rhizosheath carboxylates, and acid phosphatase activity in rhizosheath soil. Geographically, seed phytate-P concentration was the highest for the genotypes from Hainan Province, whereas it was the lowest for the genotypes from Inner Mongolia. Seed phytate-P concentration showed no correlation with any desirable root traits associated with enhanced P acquisition. Two genotypes (Siliyuan and Diliuhuangdou-2) with both low phytate concentrations and highly desirable P-acquisition traits were identified. This is the first study to show that some soybean genotypes have extremely low seed phytate concentrations, combined with important root traits for efficient P acquisition, offering material for breeding genotypes with low seed phytate-P concentrations.