Particle size reduction of raw materials is suggested to improve the extraction efficiency of pectin. However, conflicting reports have been published in literature, questioning to what extent particle size reduction is beneficial. This study investigated the role of reduced particle size and altered microstructure on the extraction efficiency and structure of pectin obtained from carrot pomace. High shear mixing and high pressure homogenization at different pressure levels (5–100 MPa) resulted in samples with a median particle diameter between 563 μm and 68 μm. Particle size reduction was shown to increase the pectin extraction yield. High shear mixing followed by high pressure homogenization, more specifically, resulted in a 50% increase of the pectin yield, resulting in the extraction of 62% of the pectin content. Interestingly, the extent to which the extraction yield was improved was more related to changes in the microstructure than to the particle size as such, with tissue disruption leading to more outspoken changes in pectin extractability than further disintegration of cell fragments. The additional fraction of extracted pectin is thought to originate from the middle lamella rather than the primary cell wall. Overall, particle size reduction did not alter the molecular structure of the extracted pectin.