Lactic acid bacteria (LAB) are emerging as valuable agents for microbial biocontrol, due to their ability to produce broad-spectrum antagonistic compounds, including organic acids, bacteriocins, bioactive peptides, short-chain fatty acids, and volatile organic compounds (VOCs). We assessed the antifungal potential of 10 LAB strains belonging to the species Leuconostoc (Leuc.) mesenteroides and Lactiplantibacillus plantarum, isolated from five varieties of Apulian honey: i) honeydew honey, ii) French honeysuckle honey, iii) wildflower honey, iv) coriander honey, and v) eucalyptus honey. Antifungal activity was investigated through a sequential assay combining the agar overlay method and the ‘Plate-on-Plate’ technique, tested against Aspergillus (A.) niger, Penicillium (P.) crustosum, P. roqueforti, Aureobasidium (Au.) pullulans and Geotrichum spp. In both cases, all strains exhibited moderate-to-high inhibitory activity against Au. pullulans and P. roqueforti. Complete inhibition of A. niger mycelial growth was observed exclusively for Leuc. mesenteroides MME-4 in the ‘Plate-on-Plate’ assay, suggesting the involvement of bioactive VOCs within the shared headspace. The results support the application of LAB from non-conventional matrices as bioprotective agents in food and packaging systems, promoting the development of ‘green’ solutions in line with the principles of sustainability and the circular bioeconomy.