Perineuronal nets are extracellular matrix structures comprised of chondroitin and dermatan sulfate-glycosaminoglycans (CS/DS-GAGs). Histological imaging of brain PNNs is achieved using Wisteria floribunda agglutinin (WFA) labeling of PNN CS/DS-GAGs, while composition can be determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Although these methods are used to determine PNN CS/DS-GAG abundance and composition, it’s unknown whether brain fixation or processing influence these outcomes. We first explored whether tissue processing, using cryosectioning (CRYO) or paraffin embedding (PE), influence PNN analyses. Ten mice were perfused with PBS and post-fixed in 4% paraformaldehyde (PFA). Brains were cut sagittal, and one hemisphere was prepared as floating tissues (CRYO) and the second hemisphere was processed as direct mounted tissues (PE). Histochemical analyses show a 78.9% reduction in hippocampal WFA+ PNNs in the PE processed hemisphere compared to CRYO processed side. LC-MS/MS analysis of hippocampal CS/DS isomers also showed differences between each method. In a second cohort of mice, we determined that fixative (4% PFA vs 10% formalin) did not influence hippocampal WFA or CS/DS isomers between groups, suggesting tissue processing (not fixative) influences PNN analyses. We then explored whether we could correct for these CS/DS baseline differences. By comparing CS/DS isomers isolated from CRYO vs PE processed tissues within each mouse, we discovered reproducible correction factors for each isomer. Adjusting the CRYO group using these factors normalizes baseline compositional differences between CRYO and PF groups. To determine translational relevance, we compared hippocampal CS/DS isomers between three CRYO vs PE prepared non-human primate (M. nemestrina) tissues and observe similar baseline CS/DS differences. Adjusting the CRYO prepared group using corrections factors normalizes the baseline composition. These results provide strong, translational evidence that tissue processing greatly influences both PNN glycan histology and composition analyses, and that corrections must be made to account for baseline differences before comparing groups.