Chemical investigation of the fungal strain Microdiplodia sp. isolated from the shrub Lycium intricatum led to the isolation of four new compounds: a hexahydroxanthone (2), a 2,3-dihydrochroman-4-one (3), a 7-oxoxanthone derivative (4), and a 1,4-oxazepan-7-one (5). The relative configurations of the new compounds were determined by intensive NMR investigations, notably NOESY experiments at different temperatures. The absolute configurations of the well-known fungal metabolite diversonol (1) and of other xanthone derivatives (3, 4) were established by means of TDDFT ECD calculations. Most of the metabolites were biologically active, with antibacterial activity against Legionella pneumophila and/or antifungal activity against Microbotryum violaceum.