Microencapsulated peppermint (Mentha × piperita L.) essential oil (MPEO) is a prospective botanical herbicide. A hypothesis was formulated that the type of growth substrate (vermiculite, silty clay loam or sandy loam soil) and the cultivar affect the phytotoxic potential of MPEO on maize (Zea mays L.). The pot experiments assessed the effect of varying doses of MPEO or maltodextrin, a carrier of microcapsules, mixed with the growth substrates, on maize’s emergence and early growth. The morphological analyses were supported by the measurements of total phenolics in the second leaf and roots. The MPEO revealed phytotoxic effects on maize in all of the growth substrates already at a low dose (36.0 g m−2), displayed by the delays of maize emergence, reduced growth, and biomass accumulation. Maltodextrin also caused significant reductions in biomass of maize roots. In conclusion, maize is susceptible to substrate-applied MPEO, the type of substrate and the cultivar of maize, can modify this effect to a limited extent.