Background/Objectives: This retrospective observational study assessed 36-month final apical status after primary endodontic treatment and nonsurgical retreatment performed using different nickel–titanium (NiTi) instrumentation systems and explored its association with available clinical and morphological variables. Methods: The study included 89 permanent teeth from 69 patients treated between January 2022 and January 2023. Teeth with periapical lesions and complete baseline and 36-month clinical and radiographic records were evaluated using a stringent binary endpoint in which complete healing required the absence of clinical signs or symptoms and residual apical radiolucency. Associations were examined primarily using univariable logistic generalized estimating equation (GEE) models accounting for clustering of teeth within patients, while Pearson’s chi-square tests and Cohen’s w were retained as supplementary unadjusted analyses. Because CBCT/Diagnocat information could contribute to final outcome classification when available, Diagnocat-based CBCT availability was not analyzed as an explanatory variable. Results: Complete clinico-radiographic healing at 36 months was observed in 61 teeth (68.54%). When reported separately by treatment modality, complete healing was observed in 12 of 29 primary-treatment cases (41.38%) and in 49 of 60 nonsurgical retreatment cases (81.67%). Because treatment allocation was non-random and the groups differed in case characteristics, this contrast was considered exploratory rather than an estimate of comparative treatment effectiveness. Exploratory analyses showed no evidence of an association with the NiTi instrumentation system or type of NiTi motion. Conclusions: Subgroup comparisons were exploratory, unadjusted for multiple testing, and should not be interpreted as evidence of independent prognostic effects. Final apical status should therefore be interpreted within the broader context of treatment indication, tooth morphology, the method of outcome ascertainment, and the overall therapeutic protocol rather than attributed to a specific NiTi system.