Changes of the abundance of caprine milk oligosaccharides (CMO) at different lactation stages have been evaluated by hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC-Q MS) and nanoflow liquid chromatography-quadrupole-time-of-flight mass spectrometry (nano-LC-Chip-QTOF MS). Eight major oligosaccharides (OS) were quantified at different lactation stages by HILIC-Q MS, while the use of nano-LC-Chip-QToF MS allowed expanding the study to forty-nine different OS by monitoring neutral non- and fucosylated species, as well as acidic species containing not only N-acetyl-neuraminic acid or N-glycolyl-neuraminic acid residues but also the combination of both sialic acids. Overall, the most abundant OS decreased with lactation time, whereas different trends were observed for minor OS. 6'-Sialyl-lactose was the most abundant acidic OS while galactosyl-lactose isomers were identified as the most abundant neutral OS. This is the first time that a comprehensive study regarding the changes of the abundance of CMO, both neutral and acidic, at different lactation stages is carried out.