Background: Cryopreserved semen and embryos are essential tools in livestock reproduction, enabling genetic improvement and herd management. Although these materials are theoretically stable in liquid nitrogen (LN2), viability often decreases over time, particularly in farm settings. Micro-ice crystals (MICs) are hypothesized to form under poor LN2 handling conditions, potentially compromising the survival of frozen genetic resources. However, the extent and impact of MIC accumulation have not been thoroughly quantified. Methods: This study evaluated MIC accumulation and its effects on the viability of cryopreserved bovine semen and embryos under different LN2 storage environments and conditions. MIC content was measured by filtering 10 L of LN2 through nonwoven fabric and weighing the retained crystals and debris. The viability of sperm and embryos were assessed using a computer-assisted semen analysis (CASA) and blastocoel re-expansion. Results: MIC content was 3.5 times higher in farm-stored LN2 than in laboratory LN2, with significantly more debris also detected. Progressive motility and velocity parameters (VCL, VAP, VSL) were similarly reduced. Blastocyst survival dropped significantly under farm conditions after six months (42.4%) compared to laboratory storage (84.4%, p < 0.05). These findings suggest a strong correlation between MIC accumulation and decreased post-thaw viability of cryopreserved materials. Conclusions: MICs formed in LN2 due to environmental exposure and poor handling can severely impair the viability of cryopreserved sperm and embryos. Regular filtration and improved LN2 management, especially in farm environments, are essential to reduce MIC-related damage. These practices may enhance the long-term usability and reliability of genetic resources in livestock breeding programs.