The use of fertilizers in agriculture is vital for crop growth and yield particularly in nutrient-limited soils. However, fertilizer application has been found to increase heavy metal (HM) contents which could affect the crop and soil quality. This study aimed to determine selected HMs concentrations in 11 commercially available fertilizers in Brunei Darussalam, comprising of organic (poultry manure, sheep manure and compost) and inorganic (seven NPK fertilizers and urea) fertilizers using an inductively coupled plasma-optical emission spectroscopy. All fertilizers had metal concentrations that were mostly below the standard safety limits. The highest average metal concentration in all fertilizers was Al, particularly in sheep manure but there are no standard safety limits set for Al. The Cd contents in inorganic fertilizers (NPK + Mg + TE 12:12:17:02, NPK + TE 15:15:15 and NPK 13:13:21) were above the permissible safety limits of China and Japan (8 mg kg−1) but below the safety guidelines set by Australia, Canada and European Commission. The Cd, Co, Cr, Mn, Ni and Pb levels were found to be the highest in NPK + Mg + TE 12:12:17:02 than all the other fertilizers while the highest levels of Fe and Al, and Cu and Zn were observed in the sheep manure and poultry manure, respectively, relative to other fertilizers. Almost all HMs analyzed was highly correlated with each other, suggesting that the HMs could be present as a complex from similar sources. Hence, continuous and repeated monitoring of HM concentrations in fertilizers is recommended to assess potential health risks in plants and humans towards achieving food security.