Objective: Arthrodesis of the first metatarsophalangeal joint (MTPJ) is a reliable procedure for treating various pathologies related to this joint. However, non-union is a common and debilitating complication of the procedure. The purpose of this study was to assess whether the use of a mechanical reamer to prepare the joint surface increases the risk of non-union compared to traditional manual osteotomy. Methods: A retrospective study of all patients who underwent their first MTPJ arthrodesis surgery in our medical center between 2010 and 2015. The articular surface preparation of the MTPJ was either manually performed (Group 1) or mechanically conducted with reamers (Group 2). Data regarding demographic characteristics, indications for surgery, osteosynthesis methods, and post-operative complications, including non-union, infection, and revision rates, were collected for all patients. Results: A total of 83 patients with 92 primary first MTPJ arthrodesis (44 cases in Group 1 and 48 cases in Group 2) were included with a mean follow-up time of 45.3 months (SD 16.8). The two groups were comparable in terms of age, gender, comorbidities, indication for surgery, and follow-up time. The non-union rate was 15.9% in Group 1 and 25% in Group 2 (p = 0.28). Group 2 showed a significantly higher rate of revision surgery compared to Group 1 (43.7% vs. 22.7%, p = 0.03). Conclusions: The mechanical reamer group had a higher non-union rate and a significantly higher rate of revision surgery compared to low-energy manual joint preparation. In light of these findings, the use of mechanical reamers for joint preparation in the first MTPJ arthrodesis was discontinued at our medical center.