In recent decades, there has been growing interest in exploring the soil biota, highlighting the significance of soil organisms’ networks in soil functioning. Here, we use a modeling approach to investigate how changes in cropping practices influence the soil food web dynamics and it relates to that of soil functioning. In an experimental trial, we tested for change in topsoil food webs after shift from conventional to alternative practices (changes in tillage intensity, amount of residues returned and N fertilization rate). Samplings were made in 16 plots of a randomized complete block design during spring of year 0, 2 and 4 after the onset of the trial. Microorganisms, microfauna, mesofauna and macrofauna were sampled, identified and grouped into trophic groups. We built a general soil food web describing plausible carbon flows between these trophic groups and computed several network indices. At the same dates, soil functions linked to C and N dynamics were measured from soil samples. We used a COSTATIS analysis to investigate relationships between temporal sequences of soil functions and soil food web indices. Significant interactive effects of the date and of agricultural systems were found on the mean and the maximum trophic level, the bacterial-to-fungal path ratio, the total biomass and the way biomass accumulates across trophic levels, the number of trophic groups and the functional redundancy in trophic groups. Similarly, organic matter transformations and enzymatic activities showed differences across date and agricultural systems. Results show that temporal changes in soil food web structure and in soil processes related to N and C cycling co-vary following changes in agricultural management practices. Management practices related to tillage exerted stronger effects on soil food web functioning than those related to the export of crop residues or reduction in mineral N fertiliser. For instance, reduced tillage lead to more complex food webs, with increased C and N mineralization in the upper soil layer (0–5 cm), in which most of the residues accumulate. Our results provide insights on soil food webs temporal dynamics, even within a restricted panel of agricultural practices. Our results suggest that changes in agricultural practices influence feedbacks between organisms and the functions they perform, so that a temporal co-structure can be observed in the studied site. Such work could help better understand the mechanisms of resistance or ecological debt during agroecological transition, which could limit or delay expected Nature-based solutions.