One of the primary tools for cooperatively managing animal populations within the Association of Zoos and Aquariums is through Breeding and Transfer Plan (BTP) recommendations. These recommendations consider population demographics, genetics, husbandry, and institutional needs and aim to improve population viability and long‐term sustainability. However, fulfilling (i.e., completing) recommendations can be complicated by biological and logistical challenges. We examined institutional reasons for unfulfilled Breed With, Do Not Breed, Hold, and Send To recommendations collected in surveys in PMCTrack, software for tracking recommendation fulfillment, using descriptive and text‐mining methods. Overall, 73 Animal Programs used PMCTrack to distribute 2335 surveys and accrued responses from 167 zoos and aquariums from 2007 to 2019, with a response rate of 56% (n = 1307). For Breed With recommendations, common reasons were related to an individual animal's status and a pair's breeding behavior; for all other recommendation types, reasons were often management or logistical factors. Most Breed With recommendations were attempted (≥55%) but did not result in detectable pregnancy/eggs or offspring, due to pair incompatibility or not enough time to successfully produce offspring. Hold and Do Not Breed recommendations were often unfulfilled because the BTP recommendation was replaced with an interim (i.e., updated) recommendation during the inter‐planning period. Our results support the importance of some common population management practices, such as maintaining breeding pairs/groups for multiple BTPs to improve mate familiarity, examining husbandry mechanisms to promote breeding success, and making a concerted effort to adhere to planning timelines to facilitate transfers in alignment with breeding seasons.