Composting technologies have progressed parallel to the growing interest in recycling organic waste over recent decades, whilst in-field compost application requires technical improvement and more experience in order to optimize their effect according to the agro-environment and the type of crop which follow their incorporation into the soil. In response to compost application, biological soil features were assessed in field by adopting precision agricultural machinery and by limiting soil incorporation to a depth of 15 cm. A 2-year trial was carried out on two sites in the East Po valley (Northern Italy), an agricultural district which, in 2000, was classified as being on the verge of desertification, and where efforts to counteract soil organic matter decline have been underway for some decades. A green-waste compost produced in accordance with current national directives was applied in autumn 2019 and 2020 to two organic fields using precision farming machinery for compost spreading and conventional harrows for incorporation. Fields were divided into two large plots to compare the effect of compost treatment to an untreated control and were managed according to organic farming practices. Seven months after application, microbial biomass, assessed in terms of DNA, and 17 enzymatic activities were estimated by sampling root-explored soil at the vegetative stage of different seed crops for organic horticulture. A significant overall increase of biological soil activity was detected after the second application. The qualitative response varied slightly between the two sites: a higher impact of microbial biomass was observed in the site that was poorer in soil organic matter; whilst in the other, an increase of phosphatase activities contributed more to the general increase of biological activity. Findings show that, in those agricultural soils, an agronomic advantage from compost can be obtained only after repeated applications; furthermore, precision farming technologies facilitate compost application even in small, specialized farms such as those which hosted this trial.