Poor rib health in Atlantic salmon (Salmo salar L.) can lead to negative effects on welfare and fillet quality. The present research aimed to enhance the comprehension of long-term rib morphology within a broader musculoskeletal framework of harvest-sized salmon (3 kg), examining a population fed different smoltification diets. Generally, X-ray examinations revealed the highest concentration of abnormalities in the anterior-central area of the rib cage, and the mid-distal rib parts. The different diets, based on either marine (M-group) or vegetal (V-group) ingredients, modulated the morphology of the ribs in the central area of the rib cage. Compared to the V-group, the M-group had a lower prevalence of generalized radiolucency (GR) (19 vs. 26% of mid-distal rib parts), and axis deformations/malformations (12 vs. 17% of mid rib parts). Histological examination of GR, unrelated to near inflammatory processes, revealed potential degradation/transformation of central core chondrocytes to mesenchymal-like cells. The newly formed cavity progressed/expanded through osteolysis until it reached the periosteum. In parallel, there were progressive alterations of the concentric appositional growth pattern of the compact bone, with an increase of the external collagen layer under the cellular periosteum. Disorganized collagen-rich islands were also seen in the compact bone, as were signs of new osteoid deposition in the cavity. The degenerative process in GR was accompanied by an 18–20% increase in the cross-sectional diameter of the rib. The M-group presented numerically higher mechanical rib strength (p = 0.06), and phosphorus content (p = 0.07). The sensitivity of rib morphology to smoltification diet was higher than vertebrae in the long-term. This study enhances understanding of the etiology of the primary morphological rib abnormalities in Atlantic salmon, particularly in GR, by providing detailed histomorphology of pathological changes. The study associates these changes with altered rib development, degeneration, and possibly osteomalacia.