The successful production of maize is fundamentally determined by a good choice of tillage type. Options include conventional tillage based on soil rotation, as well as a more recent conservation approach. Our aims were to determine the stress physiological effects of the plant remains left behind by different tillage procedures on the juvenile maize plants, combined with the effects of fungicide treatment on the seeds. These effects were followed and investigated by means of biophoton emission measurement, an in vivo and non-invasive imaging technique, along with chlorophyll content estimation, as well as microbial- and polymerase chain reaction-based identification of fungi presence. Our results confirmed the response reactions of maize triggered by a soil covering plant remains on the initial development and physiological involvement of maize. The positive effects of seed treatment on initial development are manifested only at the final stage of the experiment. The fungal microbiological analysis confirmed the dominant presence of necrotrophic parasites on plant residues, the stress-inducing properties of which were possible to monitor by biophoton emission. Furthermore, the presence of Fusarium spp. was confirmed by PCR analysis from samples treated with plant residues.