The aim of this work was to analyze and compare the adsorption and desorption processes of carbohydrates (glucose as a model molecule), polyphenols (gallic acid as a model molecule), and proteins (bovine serum albumin, BSA as a model molecule) on alginate microcapsules. The adsorption and desorption processes were described by mathematical models (pseudo-first-order, pseudo-second-order, and Weber–Morris intraparticle diffusion model for adsorption, and first-order, Korsmeyer–Peppas, and the Higuchi model for desorption) in order to determine the dominant mechanisms responsible for both processes. By comparing the values of adsorption rate (k2) and initial adsorption rate (h0) based on the pseudo-first-order model, the lowest values were recorded for BSA (k1 = 0.124 ± 0.030 min−1), followed by glucose (k1 = 0.203 ± 0.041 min−1), while the model-obtained values for gallic acid were not considered significant at p < 0.05. For glucose and gallic acid, the limiting step of the adsorption process is the chemical sorption of substances, and the rate of adsorption does not depend on the adsorbate concentration, but depends on the capacity of the hydrogel adsorbent. Based on the desorption rates determined by the Korsmeyer–Peppas model (k), the highest values were recorded for gallic acid (k = 3.66236 ± 0.20776 g beads/mg gallic acid per min), followed by glucose (k = 2.55760 ± 0.16960 g beads/mg glucose per min) and BSA (k = 0.78881 ± 0.11872 g beads/mg BSA per min). The desorption process from alginate hydrogel microcapsules is characterized by the pseudo Fickian diffusion mechanism.