Microgreens are a new, rapidly growing group of foodstuffs. The decorative function of these is often accompanied by their use in traditional dishes. As microgreens are eaten at very early stages, when the development of the epidermis is at its minimum, the bioavailability of minerals will be found to be higher in microgreens then in mature vegetables. So, microgreens can be an excellent functional food, especially for mineral-deficient populations, although they can also be a source of contaminants such as heavy metals or nitrates and nitrites. The purpose of this study was to measure the levels of selected heavy metals (i.e., cadmium, arsenic, lead, chromium, aluminium, zinc, copper, cobalt, molybdenum, manganese, vanadium, boron, antimony, thallium, titanium and strontium), as well as nitrates and nitrites, in microgreens at various stage of vegetation, using uncommon oilseed plants like nigella—Nigella sativa L., safflower—Carthamus tinctorius L., and camelina—Camelina sativa L. The examined microgreens of rare oilseed plants may be a source of contaminants and nitrates. The mineral profile of these plants is mainly determined by their genotype. Microgreens’ cultivation involves compliance with safety standards and replicable conditions to guarantee that the highest nutritional value is reached at the lowest possible contaminant level.