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This paper examined the relationships between motivation and achievement in a first-year problem-based, psychology program (N = 881). Motivation and academic achievement were measured during the first half (Time 1) and the second half of the first year (Time 2). Our results indicated that autonomous motivation (i.e., studying out of interest or meaningfulness) declined, whereas amotivation increased during the first year. With a cross-lagged panel model, we examined reciprocal relationships between motivation and achievement (i.e., professional behavior in group meetings and examination grades). Autonomous motivation and amotivation were associated with achievement on the short-term but did not predict long-term achievement. However, amotivation and autonomous motivation at the end of the year were affected by students’ prior achievement.