The developmental trajectory of learning during residency may be attributed to multiple factors, including variation in individual trainee performance, program-level factors, graduating medical school effects, and the learning environment. Understanding the relationship between medical school and learner performance during residency is important in prioritizing undergraduate curricular strategies and educational approaches for effective transition to residency and postgraduate training. This study explores factors contributing to longitudinal and developmental variability in resident Milestones ratings, focusing on variability due to graduating medical school, training program, and learners using national cohort data from emergency medicine (EM) and family medicine (FM). Data from programs with residents entering training in July 2016 were used (EM: n=1,645 residents, 178 residency programs; FM: n=3,997 residents, 487 residency programs). Descriptive statistics were used to examine data trends. Cross-classified mixed-effects regression were used to decompose variance components in Milestones ratings. During postgraduate year (PGY)-1, graduating medical school accounted for 5% and 6% of the variability in Milestones ratings, decreasing to 2% and 5% by PGY-3 for EM and FM, respectively. Residency program accounted for substantial variability during PGY-1 (EM=70%, FM=53%) but decreased during PGY-3 (EM=62%, FM=44%), with greater variability across training period in patient care (PC), medical knowledge (MK), and systems-based practice (SBP). Learner variance increased significantly between PGY-1 (EM=23%, FM=34%) and PGY-3 (EM=34%, FM=44%), with greater variability in practice-based learning and improvement (PBLI), professionalism (PROF), and interpersonal communication skills (ICS). The greatest variance in Milestone ratings can be attributed to the residency program and to a lesser degree, learners, and medical school. The dynamic impact of program-level factors on learners shifts during the first year and across the duration of residency training, highlighting the influence of curricular, instructional, and programmatic factors on resident performance throughout residency.