(1) Background: Coffee agroforestry systems (CAFS) in Veracruz, Mexico, are being displaced by avocado monocultures due to their high economic value. This change can generate alterations in the type of organic residues produced and soil biological activity (SBA) which is sensitive to climatic variations, changes in floristic composition, and agronomic management. It can be evaluated through soil respiration and macrofauna, both related to soil carbon (C) and nitrogen (N) dynamics. The objective was to:(1) Analyze the variation of SBA as well as the C and N dynamics in modified coffee agroforestry systems;(2) Methods: Three CAFS (renewed, intensive pruning, and with the introduction of avocados) and an avocado plantation were compared. The evaluations were conducted during the period 2017–2019. Soil parameters (respiration, macrofauna, C and N contents) and C content of plant biomass were measured in plots of 25× 25 m 2 from three soil depths in triplicate. Spearman’s test and a principal component analysis were performed to determine the structural dependence on C and N dynamics;(3) Results: The introduction of avocado showed the lowest soil respiration values (with 193 g CO 2 ha− 1 h− 1 at 0–10 cm depth), this system did not display soil macrofauna and increased soil organic carbon content. The soil C/N ratio was sensitive to the introduction of avocado. Correlation between soil respiration and litter-related parameters was positive, but it was negatively correlated with soil organic matter and total soil nitrogen, explaining 67.7% of the variation;(4) Conclusions: Modification of CAFS generated variations in the SBA and soil C and N contents.