Zeolite crystallization predominantly occurs by nonclassical pathways involving the attachment of complex (alumino)silicate precursors to crystal surfaces, yet recurrent images of fully crystalline materials with layered surfaces are evidence of classical growth by molecule attachment. Here we use in situ atomic force microscopy to monitor three distinct mechanisms of two-dimensional (2D) growth of zeolite A where we show that layer nucleation from surface defects is the most common pathway. Direct observation of defects was made possible by the identification of conditions promoting layered growth, which correlates to the use of sodium as an inorganic structure-directing agent, whereas its replacement with an organic results in a nonclassical mode of growth that obscures 2D layers and markedly slows the rate of crystallization. In situ measurements of layered growth reveal that undissolved silica nanoparticles in the synthesis medium can incorporate into advancing steps on crystal surfaces to generate defects (i.e., amorphous silica occlusions) that largely go undetected in literature. Nanoparticle occlusion in natural and synthetic crystals is a topic of wide-ranging interest owing to its relevance in fields spanning from biomineralization to the rational design of functional nanocomposites. In this study, we provide unprecedented insight into zeolite surface growth by molecule addition through time-resolved microscopy that directly captures the occlusion of silica nanoparticles and highlights the prevalent role of defects in zeolite crystallization.