AbstractGrowing animals should allocate their limited resources in ways that maximize survival. Seabird chicks must balance the growth of features and fat reserves needed to survive on land with those needed to successfully fledge and survive at sea. We used a large, 34‐year dataset to examine energy allocation in Magellanic penguin chicks. Based on the temporal trends in the selective pressures that chicks faced, we developed predictions relating to the timing of skeletal feature growth (Prediction 1), variation in skeletal feature size and shape (Prediction 2), and responses to periods of high energetic constraint (Prediction 3). We tested our predictions using descriptive statistics, generalized additive models, and principal component analysis. Nearly all of our predictions were supported. Chicks grew their feet first, then their flippers. They continued to grow their bill after fledging (Prediction 1). Variance in feature size increased in young chicks but declined before fledging; this variance was largely driven by overall size rather than by shape (Prediction 2). Chicks that died grew slower and varied more in feature size than those that fledged (Prediction 2). Skeletal features grew rapidly prior to thermoregulation and feet and flippers were 90% grown prior to juvenile feather growth; both thermoregulation and feather growth are energetically expensive (Prediction 3). To avoid starvation, chicks prioritized storing mass during the first 10 days after hatching; then, the body condition of chicks began to decline (Prediction 3). In contrast to our prediction of mass prioritization in young chicks, chicks that were relatively light for their age had high skeletal size to mass ratios. Chicks did not show evidence of reaching physiological growth limits (Prediction 3). By examining energy allocation patterns at fine temporal scales and in the context of detailed natural history data, we provide insight into the trade‐offs faced by growing animals.