The shrinkage behavior of alkali-activated materials (AAMs) is governed by the combined effects of precursor type, activator chemistry, and curing conditions, which control microstructure development and hydration gel formation. The synergistic interaction between these two factors ultimately dictates the material’s shrinkage behavior. Due to the varying reaction kinetics of raw materials, short-term shrinkage measurements often fail to capture the long-term effects of these influencing factors on the material’s dimensional stability. In this work, slag/fly ash-based AAM with varying alkali contents were cast and subjected to different durations of sealed curing before long-term drying shrinkage tests (up to one year). Pore structure and gel chemistry were analyzed to decouple their roles in shrinkage behavior. Results show that prolonged initial curing drastically reduces shrinkage, while early exposure to drying accelerates shrinkage kinetics. When exposed to drying at an early age, mixes with higher fly ash content exhibited the greatest shrinkage after one year, whereas if cured for a longer duration, mixes with higher slag content exhibited the highest shrinkage strain. Shrinkage–mass loss relationships followed a three-stage S-curve, reflecting the combined effects of pore structure and gel characteristics. By isolating specimens with comparable pore structures at the time of exposure, gel characteristics were shown to directly govern shrinkage, with higher Na/Si ratios disrupting the C-(N)-A-S-H gel network and increasing shrinkage. Thus, this work bridges microstructural insights with practical mix design, enabling the development of AAM binders with reduced shrinkage and improved durability.