Background: The use of free gracilis muscle flaps in reconstructive surgery of the lower leg is common practice to cover defects. However, there is still a lack of understanding of the morphometric changes that occur in the transferred muscle and area of interest over time, particularly the characteristic volume decrease that is observed over the course of the first year. This study aimed to assess volume changes in patients with free gracilis muscle flap reconstruction following infection, trauma, or malignancies of the lower extremity. Methods: Three-dimensional surface imaging was performed intraoperatively after 2 weeks, 6 months, and 12 months with the Vectra H2 system. A total of 31 patients were included in this study and analyzed. Results: There was an average volume increase of 146.67 ± 29.66% 2 weeks after reconstruction. Compared to this volume increase, there was a reduction of 108.44 ± 13.62% after 12 months (p < 0.05). Overall, we found a shrinkage to 85.53 ± 20.14% of the intraoperative baseline volume after 12 months. Conclusions: The use of non-invasive 3D surface imaging is a valuable tool for volume monitoring after free flap reconstruction of the lower extremity. The free gracilis muscle flap undergoes different phases of volume change over the first year, with the greatest influence on overall change being the development and decongestion of edema. Precise initial surgical tailoring is crucial for optimal long-term functional and cosmetic results.