Key message <p>The modular organization of the conifer stem is established between needle primordia initiation in the bud through flush the subsequent spring, with elaboration on the early plan in following years.</p> Abstract <p>Plant stems are organized in modular units or phytomers, composed of a node (leaf or leaves), axillary bud and internode. In conifers, these modules, also termed stem units (SUs), develop over multiple growing seasons. Needle primordia are initiated in a vegetative bud at the distal end of a branch in the summer/fall of one year (Y1). This tissue then expands and differentiates during spring/summer flush the following year (Y2), generating the branch’s annual longitudinal growth. Previous studies explored the relation between the SU modules and overall stem length in Y2. We extend the work back into Y1, showing that stem length already depends, weakly but significantly, on needle count and SU length by the end of Y1. Needle count becomes a significantly stronger predictor of stem length in Y2. Longitudinal changes from the compact Y1 shoot apex to the extended Y2 stem are associated with radial tissue differentiation. Y1 needle primordia are initiated at the surface. Radial tissue layers are present but simple as flush begins in Y2. By the end of Y2 flush extension these have become far more differentiated, with distinct inner and outer cortex, vascular cambium, and localized lignification. SUs incorporate cells originally from the shoot apical meristem and the rib meristem and thus extend from the margin to the stem centre. This work provides new data on the early Y1 and Y2 developmental events that establish the modular organization of the branch.</p>