Reproductive biotechnologies, such as embryo transfer (ET) and fixed-time artificial insemination (FTAI), are increasingly adopted to enhance genetic progress in tropical cattle production systems. However, the high prevalence of reproductive infectious diseases in tropical regions may compromise reproductive outcomes. This study evaluated the impact of eight reproductive pathogens (Neospora caninum, Leptospira spp., Anaplasma spp., Babesia spp., Trypanosoma spp., BVDV, IBR, and BLV) on pregnancy success, embryonic loss, and abortion in 296 bovine females subjected to ET and FTAI in Huila, Colombia. Animals were classified into six genetic groups and monitored for pregnancy at 45 and 90 days post-treatment. Logistic regression models were used to evaluate associations between disease prevalence and reproductive outcomes. Neospora caninum emerged as the most detrimental pathogen, significantly reducing pregnancy rates (OR = 0.443; p = 0.034) and increasing both embryonic loss (OR = 7.35; p = 0.073) and abortion risk (ET: OR = 20.3; p = 0.0002; FTAI: OR = 3.95; p = 0.0436). Leptospira spp. and BLV were also associated with increased embryonic losses, whereas Babesia spp. and IBR were linked to a reduced risk of embryo resorption because of enhanced care, monitoring, or vaccination. Creole cattle showed lower disease susceptibility than crossbred or commercial breeds. These findings highlight the need for comprehensive disease control, targeted vaccination, and reproductive planning to improve biotechnology outcomes in tropical cattle systems.