In this paper, the adsorption of Evans blue (EB) and methyl orange (MO) azo dyes on four greenly synthesized magnetite nanoparticles has been studied to investigate the effect of the mediating plant extract's acidity on magnetite surface reactivity in azo dye adsorption. Magnetite surface reactivity has been studied through the analysis of preferential attachment of dye chromophore and auxochrome groups on magnetite nanoparticles, and adsorption yields. According to the contents of chromophore and auxochrome groups in dye structures, the mediating plant extract's acidity effect on acid site types and densities was also deduced. Used plants for the green synthesis were: Artemisia herba-alba (L), Matricaria pubescens (L), Juniperus phoenicea (L), and Rosmarinus officinalis (L), and their extract pHs were respectively 5.25, 5.05, 4.63, and 3.69. The four greenly synthesized samples of magnetite were characterized by XRD, SEM, ATR-FTIR, and UV-Vis techniques. The novelty of this paper lies in highlighting the influence of the mediating plant extract's acidity on the greenly synthesized magnetite surface reactivity towards the preferential attachment of chromophore and auxochrome functional groups in azo dye adsorption, where obtained results show that the mediating plant extract's acidity has a clear effect on the preferential attachment of chromophore and auxochrome groups on magnetite surfaces as well as on azo dyes' adsorption yields and capacities. Indeed, the decrease in the plant extract's acidity leads to an increase in the attachment of chromophore groups and a decrease in the attachment of auxochrome groups. So, it leads to an increase in Lewis acid site density and a decrease in Brønsted acid site density of magnetite surfaces. Also, the decrease of the plant extract's acidity leads to an increase in the studied dye adsorption yields, and this is because the majority of functional groups of MO and EB dyes are chromophores that attach to Lewis acid sites. The difference found in adsorption yields of EB and MO on all four magnetite samples is due to the fact that the ratio of chromophore/auxochrome groups in EB is remarkably greater than that in MO. The linear and non-linear pseudo-first-order and pseudo-second-order kinetics of the adsorption as well as the intra-particle diffusion mechanism have been analyzed. Obtained results indicate that in all adsorption processes the adsorption kinetics followed a linear pseudo-first-order kinetic model, and film diffusion is the step that controlled adsorption mechanisms. The thermodynamic studies of EB and MO adsorption processes on the four magnetite surfaces have been analyzed in the temperature range of 303.15–318.15 K. Obtained results reveal the endothermic nature of the adsorption in all cases.