Studies of postcopulatory sexual selection typically estimate a male's fertilization success from his paternity success (P2) calculated at hatching or birth. However, P2 may be affected by differential embryo viability, thereby confounding estimations of true fertilization success (F2). This study examines the effects of variation in the ability of males to influence embryo viability upon the inequality between P2 and F2. It also investigates the consequences of this inequality for testing the hypothesis that polyandrous females accrue viability benefits for their offspring through facilitation of sperm competition (good-sperm model). Simulations of competitive mating trials show that although relative measures of male reproductive success tend to underestimate the strength of underlying good-sperm processes, good-sperm processes can be seriously overestimated using P2 values if males influence the viability of the embryos they sire. This study cautions the interpretation of P2 values as a proxy for fertilization success or sperm competitiveness in studies of postcopulatory sexual selection, and highlights that the good-sperm hypothesis needs empirical support from studies able to identify and separate unequivocally the males' ability to win fertilizations from their ability to influence the development of embryos.