Studies evaluating the effects of cryopreservation on epididymal spermatozoa of Cavia porcellus remain limited. This study compared the effects of rapid and slow freezing protocols on microscopic characteristics, morphometry, and morphometric correlations. Epididymal spermatozoa from twelve guinea pigs were diluted in OptiXcell^® extender with 25% egg yolk and equilibrated at 4 °C for 6 h. One aliquot was evaluated, while the other was cryopreserved using rapid (n = 5) or slow (n = 7) protocols. After thawing, motility, viability, plasma membrane functionality, acrosomal and chromatin integrity, and morphometry were assessed; cooling profiles were characterized using linear and cubic regression models. Cryopreservation reduced microscopic parameters compared with refrigerated samples (p < 0.05). Comparison showed no significant differences in motility, viability, acrosomal integrity, or plasma membrane function (p > 0.05), whereas chromatin integrity was higher after slow freezing (p = 0.03). Rapid freezing reduced acrosomal area, acrosomal perimeter, and head length, whereas slow freezing preserved morphometric variables and correlations, although correlation patterns should be interpreted as associations among morphometric traits rather than structural preservation. Both cooling curves were well described by linear and cubic models. Slow freezing was associated with better preservation of chromatin integrity and selected morphometric characteristics.