Arthrospira spp. (known commercially as Spirulina) and Chlorella spp., valued for their evidence-based nutritional and bioactive properties, are cultivated for the purpose of production of food supplements for worldwide distribution. However, the quality and safety of the final product depends on culturing and manufacturing conditions. The present study investigated the content of toxic elements (As species, Al, Cd, Hg, Ni, Pt, Pb, Cr (VI), rare earth elements) and minerals (Ca, Co, Cr, Cu, Fe, K, Na, Mg, Mn, P, Zn) in Chlorella (n = 10) and Spirulina (n = 13) food supplements registered in the European Union. Considering the most common recommended daily dosage 3.0, supplementation with any of the studied product would contribute significantly to mineral intake, with the exception of Fe which was found at high but acceptable levels in both Spirulina and Chlorella formulas. The majority of products revealed agreement between factual mineral content and that declared on the label, the only exception being Cu content in Chlorella products found to be significantly higher (> 130%). All studied supplements were found to have Cd, Hg, and Ni levels much below safety limits, although selected ones were characterized by increased content of Al, Pb, and inorganic As. No hexavalent Cr was detected in the studied products. The study highlights that microalgal supplements can be safe for consumers if appropriate measures are taken to ensure consumer safety, although it underlines the continuous need to monitor these products in order to fully eliminate those of low quality.