Automotive thermoelectric generators (ATEGs) are devices used to harvest waste energy from the exhaust gases of internal combustion engines. An ATEG is essentially formed by three main elements: (1) heat absorber in contact with exhaust gases; (2) thermoelectric modules that directly convert heat into electricity; (3) heat sink to increase the heat transfer through the system. Thermoelectric modules (TEM) are commonly based on small-scale commercial units, with tenths of them needed to assemble a full ATEG device. Thus, several thermal and electrical connections between TEMs can be implemented. Previous studies focused on the implications on the output power. Here, we investigated the effects of using different module connections on the energy efficiency and on the electrical outputs (voltage and current). The study was carried out numerically with ATEGs that used from 4 to 100 individual TEMs. Series, parallel and square connections were investigated under two different engine operating points. The maximum output power was obtained with overall energy conversion efficiencies on the order of 3%. Though the series connection provided the highest output power, the square configuration was the best compromise between output power and electrical characteristics (voltage and current) to successfully integrate the ATEG into the vehicle management system.