Flavones, which include apigenin, are recognized as promising candidates for the prevention of cancer metastasis due to their ability to inhibit key signaling pathways. However, the natural form of apigenin shows poor solubility and stability, which limits its therapeutic efficacy. To overcome these limitations, apigenin can be chemically modified into biflavonoids and polyapigenin derivatives using enzymes such as laccase and horseradish-derived peroxidase enzyme (HRP). The aim of this work was to polymerize apigenin using horseradish-derived peroxidase enzymes. The polymerization was carried out in a batch reactor and a microreactor, and during the process characteristic parameters such as conversion, reaction time/retention time and process stability of the enzyme were monitored. Oligomeric structure of flavonoids was confirmed by Fourier transform infrared spectroscopy (FT-IR) and high performance liquid chromatography (HPLC-DAD). In the second part of the study, the reaction kinetics of apigenin polymerization was investigated using the initial rate method and the kinetic parameters were estimated. The kinetics of apigenin polymerization catalyzed by the enzyme horseradish peroxidase was described by Michaelis–Menten kinetics. When monitoring the process stability of the enzyme, a decrease in activity was observed and the deactivation constant of the horseradish peroxidase enzyme was estimated. A suitable reactor model was proposed for the reaction carried out in a batch reactor and a microreactor, which consisted of a kinetic model, enzyme deactivation and a mass balance. The validation of the developed model was performed using two independent experiments.