Aims. We aim to investigate the stellar population properties, ages, and metal content of the globular clusters (GCs) in NGC 3311, the central galaxy of the Hydra I cluster, to better constrain its evolution history. Methods. We used integral-field spectroscopic data from the Multi-Unit Spectroscopic Explorer (MUSE) to identify 680 sources in the central region of NGC 3311 and extract their 1D spectra. An analysis of these sources in terms of morphologies, radial velocities, and emission lines allowed us to narrow down our selection to 49 bona fide GC candidates. We split these candidates into two groups depending on their projected distance to the galaxy center (R), namely inner (R ≤ 20″) and outer (R > 20″) GCs. We stacked the extracted 1D spectra of the inner and outer GC populations to increase the signal-to-noise ratios (S/Ns) of the resulting spectra and hence allow full-spectrum fitting. In addition, we also created a stacked spectrum of all GCs in NGC 3311 and one of the two most central GC candidates. Using the code pPXF, we performed a stellar population analysis on the four stacked 1D spectra, obtaining mass-weighted integrated ages, metallicities, and [α/Fe] abundances. Results. All GCs are old, with ages ≥13.5 Gyr, and they have super-solar metallicities. Looking at the color distribution, we find that the inner ones tend to be redder and more metal-rich than the outer ones. This is consistent with the two-phase formation scenario. Looking at the full-spectral fitting results, at face value the outer GCs have a larger [α/Fe] ratio, which is in line with what is found for the stars that dominate the surface brightness profile at the same radii. However, the values for outer and inner GCs are consistent within the uncertainties. Interestingly, the stacked spectrum of the two most central GCs appears to have the highest metallicity and [α/Fe], although with larger uncertainties. They might be associated with the core progenitor of NGC 3311. Conclusions. The careful analysis of the MUSE-extracted 1D spectra for compact sources in the center of NGC 3311 and its halo indicate that a significant fraction (28%) do display emission lines. Once they are removed, the selected bona fide GC candidates are old (≥13.5 Gyr) and have super-solar metallicities (slightly larger in the center) and [α/Fe] (slightly larger for the outer GCs). Stellar population analyses of the extracted spectra do not support the presence of an intermediate (a few Gigayears) GC population in the central 40 arcsec (10 kpc) radius of NGC 3311.