Objectives The purpose of this study was to evaluate the improvement of students’ ability to answer consecutive patient management problem (PMP) and modified essay question (MEQ) exams, to assess its relationship with academic progress, and to determine whether consecutive PMP-MEQ exams can improve the students’ clinical reasoning skills by improving the test scores. Methods This descriptive, analytical, cross-sectional study consisted of 67 third-year nutrition students in three consecutive years, who were asked to prepare for a multiple-choice question (MCQ) test and consecutive PMP-MEQ exams. The students were required to answer PMP-MEQ exam, which comprised of two queries of five-choice question (PMP) and three short-answer questions (MEQ). Repeated measures ANOVA, independent -test, paired -test, and Pearson’s correlation test were used for statistical analysis. Results The mean difference in PMP scores was significant between the three periods (P = 0.0001). However, the difference in the mean score of PMP exam between students with grade point average (GPA) ≥ 16 and GPA < 16 was not significant, except for PMP3 (P = 0.001). An increase was observed in the scores of students in both groups by continuous PMP examination. The significant mean difference in PMP3 exam showed that improvement of students with GPA ≥ 16 was greater than that of students with GPA < 16 (P = 0.001). The difference in the mean scores of MCQ and PMP exams was significant, except for the third PMP exam in students with GPA ≥ 16 (P = 0.143). Conclusions Use of PMP-MEQ exams in reasoning-based clinical education can be a suitable approach for clinical evaluation of undergraduate students. Also, continuous PMP-MEQ examination can improve the clinical reasoning of students, mainly those with GPA ≥ 16.