We study the interaction between a pulsar and an inhomogeneous stellar wind in gamma-ray binaries. In such systems, the acceleration of particles likely occurs at the region of collision between the two winds, which is typically assumed to be smooth. However, the early-type stars that are thought to be present in some gamma-ray binaries appear to have clumpy winds. During the two-wind interaction, these clumps arrive at the acceleration region, reshape the interaction structure, and subsequently impact the related non-thermal emission. Depending on the adopted stellar wind parameters, the clumps can produce observable fluctuations in the X-ray and gamma-ray bands. Semi-analytical calculations of the dynamical evolution and the non-thermal emission allow the study of clump-induced small-scale variability of such systems.