This study is focused on the environmental geochemistry of potentially toxic metals (PTMs)-bearing products and wastes in a mining area in Djebel Onk (NE Algeria) and their potential ecological and health risk assessment. Representative samples from (i) commercial products and (ii) grain size classes of wastes were mineralogically characterized using X-ray diffraction. The major and PTMs elements in the samples were chemically analyzed via ICP-AES and ICP-MS, respectively. The results reveal that the samples were mostly composed of carbonate fluorapatite (P2O5 > 24 wt %) and yielded PTM concentrations within the average range of phosphorites in neighboring countries and worldwide deposits as well. The concentrations of V, Cd, As, Ni, and Pb in the products were found to be within the acceptable values according to various standards, such as the Canadian and German Fertilizer Ordinance policies. Geochemically, PTMs distribution is linked to the main sub-composition of phosphate rock (apatite, clay, and dolomite). The Enrichment Factors (EF) display very-high-to-extremely-high enrichment of PTMs (Cr, Zn, As, Sr, Mo, Cd, Sb, Tl, Th, and U), while V, Co, Cu, Ni, Zr, Ga, Nb, and Pb show minor and moderate-to-high enrichments. Among all the PTMs, Cd, Tl, and U display a very high ecological risk (PERI) and contribute most to the total risk index (RI). The human health risk assessment of PTMs represented by the Hazard Index (HI) indicates that the non-carcinogenic risks are below the threshold values (HI < 1), while the HI values are higher for children than they are for adults. However, the cancer index (life time cancer risk) for Cr, Ni, As, and Cd for children and Cd for adults is greater than the acceptable threshold. These results are useful for phosphate beneficiation via removing these PTMs from the commercial product for efficient waste management.