Objective quantification of tendon structural changes through imaging is only achieved by evaluating tendon structure using ultrasound tissue characterization (UTC) technology. This study compares the effects of bone marrow mesenchymal stromal cells (BM-MSC) and leukocyte-poor platelet-rich plasma (Lp-PRP) on tendon structure and clinical outcomes in male patients with patellar tendinopathy measured with UTC at 3, 6, and 12 months after treatment. This is a double-blinded clinical trial with a randomized active control study with 20 male patients diagnosed with patellar tendinopathy who underwent BM-MSC and Lp-PRP. Bilateral ultrasound tissue characterization scans of the patellar tendon were carried out after 3, 6, and 12 months, as well as tests for strength and pain. UTC patellar tendon was analyzed at the insertion, proximal, and mid-tendon. BM-MSC showed a greater capacity to promote further positive changes than Lp-PRP. Lp-PRP presented higher disorganized echo-type II in the mid-tendon (p = 0.04; ES = 1.06) and III (p = 0.02; ES = -1.47) after 3 months in the Lp-PRP group. Similar results were seen after 6 and 12 months. Pain and strength data show improvement in the treated tendon. BM-MSC treatment demonstrates a superior capacity to promote tendon regeneration and organization, restore strength, and reduce pain compared to Lp-PRP, after 3, 6, and 12 months in male patients with patellar tendinopathy.