Nonlinear optics lies at the heart of classical and quantum light generation. The invention of periodic poling revolutionized nonlinear optics and its commercial applications by enabling robust quasi-phase-matching in crystals such as lithium niobate. However, reaching useful frequency conversion efficiencies requires macroscopic dimensions, limiting further technology development and integration. Here we realize a periodically poled van der Waals semiconductor (3R-MoS$_2$). Due to its exceptional nonlinearity, we achieve macroscopic frequency conversion efficiency over a microscopic thickness of only 1.2${\mu}$m, $10-100\times$ thinner than current systems with similar performances. Due to unique intrinsic cavity effects, the thickness-dependent quasi-phase-matched second harmonic signal surpasses the usual quadratic enhancement by $50\%$. Further, we report the broadband generation of photon pairs at telecom wavelengths via quasi-phase-matched spontaneous parametric down-conversion. This work opens the new and unexplored field of phase-matched nonlinear optics with microscopic van der Waals crystals, unlocking applications that require simple, ultra-compact technologies such as on-chip entangled photon-pair sources for integrated quantum circuitry and sensing.