Factors associated with the optimal physician resident learning are yet to be fully understood. We aimed to correlate the characteristics of residency programs with the learning perception of residents. This was a cross-sectional study using an online structured questionnaire published on social networks, enrolling physician residents from almost all specialties in Brazil. The collection tool was settled considering the current national standards of medical residency programs in Brazil and it was internally validated. The response rate was 71.4% (n = 1,419). The median age was 28 years (IQR = 27-30), 51.9% were from clinical areas and 69.9% from the first or second postgraduation year. Adequate quality of faculty supervision was reported by 50.9%; frequent supervision of assistance activities in 22.1%; proper structure for carrying out healthcare in 82.1%, formal appraisals in 81.8%, classroom activities more than three times a week in 12.3%. Learning was rated as satisfactory by 70.8%. We found an 'inverted-U' shape correlation between duty hours and learning – briefer and longer workloads were associated with unsatisfactory learning. The factors independently associated with learning satisfaction were quantity (OR = 10.79, 95%CI = 7.38-15.77) and quality (1.68, 1.19-2.37) of preceptorship, structure for healthcare (2.10, 1.44-3.08), formal evaluations (1.83, 1.26-2.67), and briefer workload (0.18, 0.04-0.90) and age (0.94, 0.89-0.99) (AUROC = 0.838, 95%CI = 0.816-0.860). We conclude that the perception of satisfactory learning was influenced by higher frequency and quality of faculty supervision, adequate structure for healthcare, formal assessments, and reduced duty hours and age. Regulatory institutions should reinforce strategies to guarantee the fulfillment of residency standards and faculties should receive continued formal training to maximize their teaching skills.