In this work, the essential oils (EOs) from Eriocephalus africanus leaf, Vitex agnus-castus leaf and fruit, Cymbopogon citratus leaf, and Rosmarinus officinalis leaf were used as antifungal agents against isolated Aspergillus flavus, Cladosporium cladosporioides, and Penicillium chrysogenum from an ancient Egyptian child’s mummy. The isolated fungi were used to colonize the samples of linen fibers. The best oil was used as a novel natural product for the cleaner production of model linen fibers similar to those used in ancient Egyptian mummification. Standard and original linen fibers were compared with the infected Linen samples using Fourier transform infrared (FTIR) and X-ray diffraction (XRD) analyses. The FTIR revealed the changes in the molecular structure of the cellulose, hemicellulose, and lignin of the infected linen fibers. The cellulose crystallinity indices decreased to 64.61%, 52.69%, and 54.63% in the linen inoculated with A. flavus, C. cladosporioides, and P. chrysogenum compared to the control sample (72.08%), thereby affecting the chemical properties of the cellulose. The mycelia inhibition percentages of the three fungi reached 100% after the leaf EO from V. agnus-castus was applied, followed by C. citratus. The V. agnus-castus leaf EO applied at contraptions of 250, 500, 50, 1000, and 2000 µL/mL showed 100% inhibition for A. flavus and P. chrysogenum and reached 100% against C. cladosporioides at concentrations of 500, 750, 1000, and 2000 µL/mL. C. citratus leaf essential oil applied at concentrations of 500, 750, 1000, and 2000 µL/mL showed 100% inhibition to the growth of A. flavus and C. cladosporioides and reached 100% inhibition against the growth of P. chrysogenum at concentrations of 750, 1000 and 2000 µL/mL. This inhibition could be related to the main compounds of caryophyllene (23.13%), eucalyptol (20.59%), sabinene (β-thujene) (12.2%), γ-elemene (9%), and β-farnesene (6.14%) identified in V. agnus-castus leaf EO or due to the main compounds of β-citral (43.63%) and geranial (41.51%), as identified in the leaf EO of C. citratus by GC/MS. The morphological changes in the hyphae of the fungi were observed via SEM examination, where V. agnus-castus leaf EO, the best active oil, showed potent inhibition to fungi grown on the model linen fiber. In this way, the morphology and the structure of the hyphae were effectively changed. Our findings prove that the designed model linen fiber treated with V. agnus-castus leaf EO is able to preserve wrapping fibres and represents a novel natural alternative for effective fungicidal treatment.