This paper presents the results of an investigation of the influence of hydrodynamic instabilities on heat transfer intensity during the condensation of R134a and R404A refrigerants in pipe mini-channels. The heat transfer coefficient h is a measure of the effectiveness of the condensation process. It is particularly important to determine the value of the coefficient in the two-phase condensation area in a compact condenser. In other condenser areas (i.e., precooling of superheated vapor and subcooling of condensate), the heat efficiency is substantially smaller. Hydrodynamic instabilities of a periodic nature have an influence on size changes in these areas. A decrease in the heat transfer coefficient h in the two-phase area results in decreased intensity of the heat removal process in the whole condenser. The experimental investigations were based on the condensation of R134a and R404A refrigerants in horizontal pipe mini-channels with internal diameters of d = 0.64; 0.90; 1.40; 1.44; 1.92; 2.30 and 3.30 mm. Disturbances of the condensation process were induced with a periodic stop and a repetition of the flow of the refrigerant. In the range of frequencies, f = 0.25–5 Hz, of the periodically generated disturbances, an unfavorable influence on the intensity of the heat transfer during the condensation process in pipe mini-channels was identified. The reduction in the intensity of the heat transfer during the condensation process, which was induced with hydrodynamic instabilities, was presented in the form of the dependence of the heat transfer coefficient h on the vapor quality x and the frequencies f of the disturbances. The influence of the refrigerant, the diameter of the mini-channels and the frequency f on the damping phenomenon of the periodical disturbances in the pipe mini-channels was identified.