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Chemical investigation of the plant-derived endophytic fungus <i>Diaporthe unshiuensis</i> YSP3 led to the isolation of four new compounds (<b>1</b>–<b>4</b>), including two new xanthones (phomopthane A and B, <b>1</b> and <b>2</b>), one new alternariol methyl ether derivative (<b>3</b>) and one α-pyrone derivative (phomopyrone B, <b>4</b>), together with eight known compounds (<b>5</b>–<b>12</b>). The structures of new compounds were interpreted on the basis of spectroscopic data and single-crystal X-ray diffraction analysis. All new compounds were assessed for their antimicrobial and cytotoxic potential. Compound <b>1</b> showed cytotoxic activity against HeLa and MCF-7 cells with IC₅₀ values of 5.92 µM and 7.50 µM, respectively, while compound <b>3</b> has an antibacterial effect on <i>Bacillus subtilis</i> (MIC value 16 μg/mL).