This paper strove to characterize and compare ejaculates collected from two geese breeds over the period of two years in the context of selected traditional, biochemical, oxidative, bacteriological, and immunological properties. Slovak white and Suchovy ganders were selected for sperm quality evaluation, while bacteria were characterized using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Oxidative profile of semen was assessed using chemiluminescent and colorimetric protocols. Levels of pro-inflammatory cytokines and antibacterial proteins were evaluated with the enzyme-linked immunosorbent assay. Seminal plasma biochemistry was assessed with an automated clinical chemistry analyzer. Overall, lower semen quality was found in the Slovak white breed and during the first year of semen collection in both breeds. At the same time, the sperm motility was in a strong positive correlation with the plasma membrane integrity (P < 0.0001), whilst being negatively associated with the bacterial load (P = 0.0056), reactive oxygen species production (P < 0.0001), DNA fragmentation (P < 0.0001) and the levels of interleukin-1 (P < 0.0001) and C-reactive protein (P < 0.0001). Higher semen quality in ganders was accompanied by increased seminal plasma levels of lysozyme (P < 0.0001), cathelicidin (P < 0.0001), calcium (P < 0.01), magnesium (P < 0.01 in the case of the Suchovy breed), phosphorus (P < 0.001), total proteins (P < 0.0001 with respect to the Slovak white breed; P < 0.01 with regards to the Suchovy breed) and cholesterol (P < 0.05), and a decreased activity of aspartate transaminase (P < 0.0001). We may conclude that semen of overall better quality was obtained during the second year of semen collection as opposed to the first year in ganders of both selected goose breeds.