This study aimed to compare the occurrence and nuisance of adverse events following administration of each COVID-19 vaccine dose between two groups: individuals given three doses of mRNA vaccine (homologous group, 3 × mRNA, n = 252) and those given two doses of adenoviral vector vaccine further boosted with mRNA vaccine (heterologous group, 2 × AZ + 1 × mRNA, n = 205). Although the studied groups differed significantly in the frequency and number of side effects after the first and second vaccine dose, no relevant differences were seen following the booster administration. Arm pain and fatigue were the most common effects, regardless of the vaccination group and vaccine dose. In the homologous group, female sex, lower BMI, and no history of regular influenza vaccination were associated with a higher frequency of side effects of a booster dose. In the heterologous group, the history of COVID-19 was associated with an increased number of side effects seen after a booster. In both groups, the number of side effects related to the first and second dose correlated with the number observed after administration of a booster dose. Individuals receiving a homologous booster reported a higher nuisance of side effects than the heterologous group. It was similar to the level reported after the second dose in both groups. The use of pharmaceuticals to counteract the side effects was more frequent after a first dose in the 2 × AZ + 1 × mRNA group, but higher after second dose in individuals receiving the 3 × mRNA vaccination scheme. The frequency of pharmaceutical use after a booster dose was similar in both groups (approx. 60%). Paracetamol was most frequently chosen, regardless of the group and vaccine dose. In addition, the vast majority of participants (93%) declared to accept future doses of the COVID-19 vaccine if their administration would be recommended. This study provides an overview of the response to homologous and heterologous mRNA vaccine booster dose that may be valuable in shaping accurate and honest communication with vaccinated individuals, especially in those regions which are yet to pursue booster strategies.