Axillary meristem fate patterns along shoots, also referred to as shoot structure, appear to be fairly consistent among trees within a genotype growing under similar conditions. Less is known about shoot structural plasticity following external manipulations, such as pruning. The aim of this study on almond (Prunus dulcis (Mill.)) shoots was to investigate how pruning severity affects the structure of 1-year-old shoots that grew after pruning (regrowth shoots), the 2-year-old portion of shoots that remained from the previous year's growth after pruning (pruned shoots), and whether regrowth shoots reiterate the structure of the original 1-year-old shoots before pruning. Three pruning severities were imposed and the structures along the different shoots were assessed by building hidden semi-Markov models of axillary meristem fates. The structures of regrowth and pruned shoots depended on pruning severity, but maintained some of the original shoot characteristics. Regrowth shoots developed more complex structures with severe pruning, but had simpler structures than original shoots indicating progressive simplification with tree age. Pruned shoot structures were affected by the severity of pruning, by the structure when the shoots were 1 year old, and probably by local competition among buds. Changes in structure due to pruning can be modelled and be predictable.