Setting: All health centres in Macenta District, rural Guinea. Objective: To compare stock-outs of vaccines, vaccine stock cards and the administration of various childhood vaccines across the pre-Ebola, Ebola and post-Ebola virus disease periods. Design: This was an ecological study. Results: Similar levels of stock-outs were observed for all vaccines (bacille Calmette-Guérin [BCG], pentavalent, polio, measles, yellow fever) in the pre-Ebola and Ebola periods (respectively 2760 and 2706 facility days of stock-outs), with some variation by vaccine. Post-Ebola, there was a 65-fold reduction in stock-outs compared to pre-Ebola. Overall, 24 facility-months of vaccine stock card stock-outs were observed during the pre-Ebola period, which increased to 65 facility-months of stock-outs during the Ebola outbreak period; no such stock-out occurred in the post-Ebola period. Apart from yellow fever and measles, vaccine administration declined universally during the peak outbreak period (August-November 2014). Complete cessation of vaccine administration for BCG and a prominent low for polio (86% decrease) were observed in April 2014, corresponding to vaccine stock-outs. Post-Ebola, overall vaccine administration did not recover to pre-Ebola levels, with the highest gaps seen in polio and pentavalent vaccines, which had shortages of respectively 40% and 38%. Conclusion: These findings highlight the need to sustain vaccination activities in Guinea so that they remain resilient and responsive, irrespective of disease outbreaks.