The purpose was to determine the coverage of maternal vaccination against influenza and pertussis, and the characteristics associated with being vaccinated, in a health area of Catalonia, Spain. Some 36,032 anonymized and computerized clinical records registries of pregnant women from Primary Care Centres (e-CAP database) were analysed, from between 2015 and 2018. Vaccination coverage and the association with sociodemographic variables and clinical conditions were estimated using a Poisson regression model. Maternal vaccination coverage against influenza ranged between 11.9% in 2015 and 6.8% in 2018, following a decreasing trend (p < 0.001). Coverage with the tetanus toxoid, diphtheria toxoid, and acellular pertussis vaccine varied between 49.8% in 2016 and 79.4% in 2018, following an increasing trend (p < 0.001). Having living children and suffering from obesity were factors associated with not being vaccinated against both infections. The predictive variables of vaccination against influenza were diabetes (IRR: 2.17, 95% CI: 1.42–3.30) and asthma (IRR: 2.05, 95% CI: 1.76–2.38); and for pertussis, it was asthma (IRR: 1.10, 95% CI: 1.03–1.17). Different socio-demographic factors and chronic conditions in pregnant women were associated with maternal vaccination, and which will have to be taken into account in clinical practice when implementing strategies to improve the coverage of the programme.