Weather conditions can profoundly affect avian reproduction. Thus far, most studies on weather effects have focused on how weather conditions prior to clutch initiation affect laying dates and, ultimately, breeding success. By contrast, little is known of how weather conditions after the onset of reproduction affect birds. Using a 32-year population study of the Blue-footed booby (Sula nebouxii) in Mexico, we show that effects of weather conditions on offspring survival and body condition at independence vary with the reproductive stage at which they occur. During most of the incubation period, warm sea surface temperatures and low to moderate rainfall depressed hatching success; while during the last month of brood care surface temperatures were unimportant but rainfall increased fledging success. In addition, chicks that experienced warm sea surface temperatures in the middle of the brood care stage had lower body condition at fledging. Our results provide insight of how weather effects vary between reproductive stages in a long-lived neotropical seabird.