The effects of a fire-retardant treatment and burl wood structure on the three-dimensional changes of aircraft sandwich panels were evaluated. Unvarnished and varnished panels with an outer decorative layer made from walnut burl (Juglans hindsii L.) were studied. Half of the samples from each type of panel received a fire-retardant treatment (phosphate-based) on all three layers of the decorative plywood. The other half had the two inner layers treated and the outer layer was left untreated. Three different wood areas formed by rotary peeling and by the grain orientation from the burl structure were identified and their veneer surfaces were separately studied. Samples pre-conditioned at 20 °C and 40% relative humidity (RH) underwent adsorption (25 °C, 90% RH) and then desorption (25 °C, 40% RH) treatments. Changes in the moisture content (MC), swelling, shrinkage, roughness, and waviness were measured after each moisture exposure condition. The results showed that the fire-retardant treatment significantly increased the MC, swelling, shrinkage, roughness, and waviness of the unvarnished and varnished panels. This treatment also affected the roughness and waviness of the burl wood structure for the unvarnished panels. The effect of this anatomical feature was not noticeable in the varnished panels.