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Background: During and after the SARS-CoV-2 (COVID-19) pandemic, many countries experienced declines in immunization that have not fully recovered to pre-pandemic levels. This study uses routine health facility immunization data to estimate variability between and within countries in post-pandemic immunization service recovery for BCG, DPT1, and DPT3. Methods: After adjusting for data reporting completeness and outliers, interrupted time series regression was used to estimate the expected immunization service volume for each subnational unit, using an interruption point of March 2020. We assessed and compared the percent deviation of observed immunizations from the expected service volume for March 2020 between and within countries. Results: Six countries experienced significant service volume declines for at least one vaccine as of October 2022. The shortfall in BCG service volume was ~6% (95% CI −1.2%, −9.8%) in Guinea and ~19% (95% CI −16%, 22%) in Liberia. Significant cumulative shortfalls in DPT1 service volume are observed in Afghanistan (−4%, 95% CI −1%, −7%), Ghana (−3%, 95% CI −1%, −5%), Haiti (−7%, 95% CI −1%, −12%), and Kenya (−3%, 95% CI −1%, −4%). Afghanistan has the highest percentage of subnational units reporting a shortfall of 5% or higher in DPT1 service volume (85% in 2021 Q1 and 79% in 2020 Q4), followed by Bangladesh (2020 Q1, 83%), Haiti (80% in 2020 Q2), and Ghana (2022 Q2, 75%). All subnational units in Bangladesh experienced a 5% or higher shortfall in DPT3 service volume in the second quarter of 2020. In Haiti, 80% of the subnational units experienced a 5% or higher reduction in DPT3 service volume in the second quarter of 2020 and the third quarter of 2022. Conclusions: At least one region in every country has a significantly lower-than-expected post-pandemic cumulative volume for at least one of the three vaccines. Subnational monitoring of immunization service volumes using disaggregated routine health facility information data should be conducted routinely to target the limited vaccination resources to subnational units with the highest inequities.