Ukraine stands as a testament to agricultural wealth due to its fertile soils, most notably, its significant share of the world’s chornozem. Rich soil is fundemantal to agricultural production, and therefore the success of the agricultural industry heavily relies on the fertility of the soil. However, modern agricultural practices in Ukraine, have led to increased anthropogenic impact on soils, affecting their biodiversity and humus content. In this regard, it is becoming increasingly important to perform comprehensive studies of microbiological, biochemical and chemical processes in the soil in response to different agricultural interventions. The urgent need to restore natural ecosystems to preserve their biodiversity and ensure ecological stability poses new scientific challenges, emphasizing the importance of urgent measures aimed at protecting the environment from pollution and degradation. This research aims to explore the effects of biodestructors on the deposition of labile carbon compounds in the soil during long-term consistent corn cultivation. The research was conducted during 2020–2023 within the framework of a stationary field experiment of the scientific research department of the «Druzhba Nova» in Varva village, Chernihiv region. The soil is a typical low-humus chornozem with the experiment focusing on a monoculture corn crop rotation. The DKC 4351 corn hybrid was sown at a density of 82 thousand units per hectare, employing a three-part experiment design: 1) a UAN control at 32–28 l/ha, 2) Ecostern Classic at 2 l/ha combined with UAN 32–28 l/ha, and 3) Ecostern Bacterial at 2 l/ha alongside Ecostern Trichoderma at 1 l/ha and UAN 32–28 l/ha. In the present study, the influence of biodestructors on soil’s agrochemical and microbiological indicators, as well as corn yield was evaluated. In a long-term stationary field experiment conducted on a typical low-humus chornozem, we investigated the influence of microbial preparations — plant residue biodestructors — on the deposition of labile carbon compounds in the soil under continuos corn cultivation. The application of Ecostern Classic and a combination of Ecostern Bacterial + Ecostern Trichoderma biodestructors resulted in an increase of labile carbon content by 0.11% and 0.18%, respectively, compared to the control. The aim of further analysis was to determinate the dynamics of the organic matter transformation coefficient, which is a marker of enhanced microbiological activity in the soil and a predominance of organic matter synthesis over its mineralization. In treatments utilizing biodestructors, this indicator was significantly higher than control values throughout the study. The survival of the fungal bioagent from Ecostern Classic and Ecostern Trichoderma bioproducts in the soil was monitored by assessing the population dynamics of the Trichoderma genus species. Results demonstrated an increase by an average of 19 thousand CFU/g with Ecostern Classic and by 34 thousand CFU/g with the combined use of Ecostern Bacterial with Ecostern Trichoderma, compared to 28 thousand CFU/g in control soil samples. This may indirectly indicate a successful colonization of the bioagent in treated soils. Using BIOTREX technology to evaluate the soil’s ecophysiological diversity, we found that the diversity index increased from 3.66 in control samples to between 4.87 and 5.61 in treatments with biodestructors. According to the further BIOTREX assessment, the use of biodestructors not only increased soil biodiversity, but also improved soil health. The application of these biodestructors also significantly boosted corn grain yield with an increase of 0.32 t/ha with Ecostern Classic treatment and 0.18 t/ha with the combined use of Ecostern Bacterial with Ecostern Trichoderma, compared to control.