Canine cranial cruciate ligament rupture (CrCLR) is a very common pathology. Surgical stabilization is the first choice treatment, although it does not fully eliminate the increased risk of osteoarthritis. This preliminary study was carried out to explore whether a newly formulated joint health supplement would benefit metabolic, clinical and radiographic changes in dogs with CrCLR surgically treated with tibial plateau leveling osteotomy (TPLO). Besides chondroitin sulfate and glucosamine hydrochloride, the studied supplement contained anti-inflammatory and antioxidant ingredients, the main ones being N-palmitoyl-D-glucosamine (Glupamid®) and quercetin. It was thus intended to target not only chondrodegenerative components of osteoarthritis, but also post-injury inflammatory response and oxidative stress of joint tissues. Thirteen dogs underwent TPLO and were randomly allocated to treatment (n = 6) and control groups (n = 7), the former receiving the joint supplement for 90 days. Lameness and radiographic osteoarthritis changes were scored before (i.e., baseline) and at 30 and 90 days post-surgery. Synovial fluid samples were collected from injured stifles at the same time points. Levels of representative metabolites were measured by proton nuclear magnetic resonance spectroscopy in a blinded fashion. In the metabolomic analysis, special attention was paid to lactate, due to its emerging recognition as a key marker of inflammation. In the last time period (from the 30th to the 90th day), lameness improved by a factor of 2.3 compared to control dogs. No significant difference was observed in the radiographic osteoarthritis score between groups. In the first postoperative month, lactate and creatine levels significantly dropped in treated compared to control dogs. Compared to surgery alone, combining the joint supplement with TPLO resulted in a trend to a better clinical outcome in the later time interval but did not influence osteoarthritis radiographic progression. A significantly better rebalance of joint microenvironment in the early time interval (baseline - 30 days) was shown by metabolomic analysis, thus suggesting that the study supplement could limit ongoing inflammatory responses.