Methylxanthines, found in the seeds, leaves, and fruits of some plants, are receiving increasing attention as promising treatments for wood-degrading fungi. The aim of the study presented herein was to explore the potential applications of caffeine, four caffeine derivatives (viz. 8-bromo-caffeine, 8-iodo-caffeine, 8-(4-fluorophenoxy)-caffeine, and 8-(2,3,5,6-tetrafluoroalcoxy)-caffeine), and theophylline as antifungals for Botryosphaeriaceae species associated with grapevine trunk diseases (GTDs). In vitro susceptibility tests were conducted to assess the antimycotic activity of the aforementioned compounds and their conjugated complexes with chitosan oligomers (COS). Caffeine, Br-caffeine, and I-caffeine exhibited higher efficacies than imidazole, the chosen antifungal control. Moreover, a strong synergistic behavior between COS and the methylxanthine derivatives was observed. The COS–I-caffeine complex showed the best overall performance against the phytopathogenic fungi with EC90 values of 471, 640, and 935 µg mL−1 for D. seriata, D. viticola, and N. parvum, respectively. In a second step, combinations of the new treatments with imidazole were also explored, resulting in further activity enhancement and EC90 values of 425, 271, and 509 mL−1 against D. seriata, D. viticola, and N. parvum, respectively, for the COS–I-caffeine-imidazole ternary compound. Given the high in vitro efficacy of these formulations for the control of GTDs, they may deserve further investigation with in vivo and field bioassays as an alternative to conventional fungicides.