Background The aim of this study is to estimate the immediate and lasting effects of the 2014–2015 Ebola virus disease (EVD) outbreak on public-sector primary healthcare delivery in Liberia using 7 years of comprehensive routine health information system data. Methods and findings We analyzed 10 key primary healthcare indicators before, during, and after the EVD outbreak using 31,836 facility-month service outputs from 1 January 2010 to 31 December 2016 across a census of 379 public-sector health facilities in Liberia (excluding Montserrado County). All indicators had statistically significant decreases during the first 4 months of the EVD outbreak, with all indicators having their lowest raw mean outputs in August 2014. Decreases in outputs comparing the end of the initial EVD period (September 2014) to May 2014 (pre-EVD) ranged in magnitude from a 67.3% decrease in measles vaccinations (95% CI: −77.9%, −56.8%, p < 0.001) and a 61.4% decrease in artemisinin-based combination therapy (ACT) treatments for malaria (95% CI: −69.0%, −53.8%, p < 0.001) to a 35.2% decrease in first antenatal care (ANC) visits (95% CI: −45.8%, −24.7%, p < 0.001) and a 38.5% decrease in medroxyprogesterone acetate doses (95% CI: −47.6%, −29.5%, p < 0.001). Following the nadir of system outputs in August 2014, all indicators showed statistically significant increases from October 2014 to December 2014. All indicators had significant positive trends during the post-EVD period, with every system output exceeding pre-Ebola forecasted trends for 3 consecutive months by November 2016. Health system outputs lost during and after the EVD outbreak were large and sustained for most indicators. Prior to exceeding pre-EVD forecasted trends for 3 months, we estimate statistically significant cumulative losses of −776,110 clinic visits (95% CI: −1,480,896, −101,357, p = 0.030); −24,449 bacille Calmette–Guérin vaccinations (95% CI: −45,947, −2,020, p = 0.032); −9,129 measles vaccinations (95% CI: −12,312, −5,659, p < 0.001); −17,191 postnatal care (PNC) visits within 6 weeks of birth (95% CI: −28,344, −5,775, p = 0.002); and −101,857 ACT malaria treatments (95% CI: −205,839, −2,139, p = 0.044) due to the EVD outbreak. Other outputs showed statistically significant cumulative losses only through December 2014, including losses of −12,941 first pentavalent vaccinations (95% CI: −20,309, −5,527, p = 0.002); −5,122 institutional births (95% CI: −8,767, −1,234, p = 0.003); and −45,024 acute respiratory infections treated (95% CI: −66,185, −24,019, p < 0.001). Compared to pre-EVD forecasted trends, medroxyprogesterone acetate doses and first ANC visits did not show statistically significant net losses. ACT treatment for malaria was the only indicator with an estimated net increase in system outputs through December 2016, showing an excess of +78,583 outputs (95% CI: −309,417, +450,661, p = 0.634) compared to pre-EVD forecasted trends, although this increase was not statistically significant. However, comparing December 2013 to December 2017, ACT malaria cases have increased 49.2% (95% CI: 33.9%, 64.5%, p < 0.001). Compared to pre-EVD forecasted trends, there remains a statistically significant loss of −15,144 PNC visits within 6 weeks (95% CI: −29,453, −787, p = 0.040) through December 2016. Conclusions The Liberian public-sector primary healthcare system has made strides towards recovery from the 2014–2015 EVD outbreak. All primary healthcare indicators tracked have recovered to pre-EVD levels as of November 2016. Yet, for most indicators, it took more than 1 year to recover to pre-EVD levels. During this time, large losses of essential primary healthcare services occurred compared to what would have been expected had the EVD outbreak not occurred. The disruption of malaria case management during the EVD outbreak may have resulted in increased malaria cases. Large and sustained investments in public-sector primary care health system strengthening are urgently needed for EVD-affected countries., Bradley Wagenaar and colleagues use health facility data to analyze losses to essential primary healthcare service outputs during and immediately after the EVD outbreak, and their recovery in the years after., Author summary Why was this study done? Almost 2 years after the final case of Ebola virus disease (EVD) was discharged in Liberia, it is essential to understand the lingering effects of the EVD outbreak on the public-sector primary healthcare system. Existing studies of the effects of the EVD outbreak on population health and health system functioning have relied on small survey samples, mathematical modeling approaches, and data collected at single points in time before, during, or immediately after the epidemic rather than using health system output data to understand long-term system trends. We aimed to improve on these limitations and extend existing analyses to cover a census of health facilities in Liberia (excluding Montserrado County) from January 2010 to December 2016. What did the authors do and find? We used health facility data across a census of facilities and over an 84-month period to analyze changes in essential primary healthcare service indicators during and after the EVD outbreak. We found that it took only 4 months (June–September 2014) to lose between 35% and 67% of essential primary care health system outputs across Liberian clinics, and that, as of November 2016 (19 months post-EVD), all health system indicators had recovered to their pre-EVD levels. Given that health system outputs are time-limited, the loss of an estimated 776,110 clinic visits, 24,449 bacille Calmette–Guérin vaccinations, 9,129 measles vaccinations, 12,941 first pentavalent vaccinations, 5,122 institutional births, 17,191 postnatal care visits within 6 weeks of birth, 101,857 artemisinin-based combination therapy treatments for malaria, and 45,024 treatments of acute respiratory infections due to the EVD outbreak will continue to severely affect population health. We estimate that the number of malaria cases treated has increased by 49% from December 2013 to December 2016—a finding potentially due to increases in the transmission of the disease following large-scale treatment interruptions during the EVD outbreak. What do these findings mean? These findings add to the body of literature suggesting that the 2014–2015 EVD outbreak across West Africa had devastating effects on the delivery of all types of public-sector primary healthcare services. For most primary healthcare indicators, it took more than 1 year post-EVD to recover to pre-EVD levels, with net losses persisting as of December 2016. Malaria cases may have increased since the EVD outbreak in Liberia, as predicted from previous modelling efforts across EVD-affected countries; the extent to which a similar trend for malaria has been recorded in Sierra Leone or Guinea is not clear. Public-sector primary healthcare system strengthening is urgently needed across West Africa, with specific focus targeted to general outpatient care, childhood vaccination, maternal health, and malaria prevention/treatment.