Source identification and quality monitoring of soil nutrients and beneficial elements (NBEs) are crucial for agricultural production and environmental protection. In this study, grid sampling (223 topsoil samples and 223 subsoil samples) was carried out in the Tongzhou District of Beijing. The concentration level of representative NBEs (N, P, K, Ca, Mg, Se, V, Ge, Mn, Zn) and some typical soil properties representing indicators (total organic carbon, TFe2O3, Al2O3/SiO2, and pH) in soils and their spatial distribution were analyzed. The major sources contributing to these NBEs were assessed by principal component analysis (PCA), redundancy analysis (RDA), and positive matrix factorization (PMF) analysis. The results suggested that the soil parent material contributed 40.09-69.84% to Zn, V, Ge, Mn, F, and K in soils; the local external source contributed 54.89-75.04% to N, Se, and TOC; and the hydrous system contributed 40.67-77.31% to Ca and Mg. The enrichment degree of each NBE was calculated using the standardized concentration ratio method. These indices exhibited the influence and mixing process of different sources on the target NBEs in topsoils. The individual concentrations of the target NBEs and the combined concentrations of N, P, and K were used to evaluate the soil quality. Our study estimated the relative contributions from dominant sources to NBEs in soils from a typical suburban area, providing a basis for agricultural activities and environmental protection.