Social life and lifelong partner commitments are expected to favor thorough partner choice, as an ill-suited partnership may have long-term consequences, adversely affecting the parents and spanning several cohorts of offspring. Here, we used ~1400 termite incipient colonies to estimate the short- and long-term costs of inbreeding upon the survival of the parents over a 15-month period, their productivity, and the resistance of their offspring toward pathogen pressure. We observed that foundation success was not influenced by the relatedness of partners, but by their levels of microbial load. We showed faster growth in inbred colonies, revealing a potential tradeoff with pathogen susceptibility. Yet, inbreeding takes its toll later in colony development when incipient colonies face pathogen pressure. Although the consequences of choosing a lifetime partner is initially determined by the partner’s health, the cost of inbreeding in incipient colonies favors outbred colonies reaching maturity