Since 1993 the Venezuelan government has implemented an intensive management program aiming to increase the population size of the endangered giant South American turtle (Podocnemis expansa). Including nest relocation and a year of captive rearing of hatchlings, the program affects the main Venezuelan P. expansa population, located in the middle Orinoco River. Although the program seems to be increasing recruitment of new individuals into the population, the effects of such nest relocation on long-term fitness-correlated parameters have not been addressed. Here we measured posthatching mortality, presence of morphological abnormalities, first-year body growth rate, and locomotive performance of juvenile turtles subjected to this management program. Nest relocation had a profound influence on juvenile P. expansa turtles, affecting their mortality, morphology, body growth rate, and locomotive performance. Transplanted clutches showed higher hatchling mortality and higher incidence of morphological abnormalities, though higher growth rates than nontransplanted clutches. Likewise, juvenile turtles coming from nontransplanted clutches appeared to run faster than those coming from transplanted nests. Clutch manipulation seemed to be responsible for the occurrence of morphological abnormalities and the increased mortality. Higher temperatures, on the other hand, may be the cause for the observed higher body growth rates in transplanted nests. Our results suggest that future management efforts minimizing the effects of clutch manipulation will not only prevent clutch losses but also enhance the long-term survival of neonates.