Background When faced with plantar defects, reconstruction of the weight-bearing areas presents unique surgical challenges. Several free flap modalities have been described in this respect, but there remains debate regarding the best-suited flap modality. Aim of this study was to compare free muscle and non-neurotized fasciocutaneous flaps for plantar reconstruction with respect to long-term functional outcomes. Methods Overall, 89 patients received 100 free flaps (anterolateral thigh [ALT] n = 46; gracilis n = 54) for plantar reconstruction. The data were screened for patients' demographics, as well as perioperative details. Postoperative complications were accounted for and the two groups compared accordingly. All patients were contacted for a long-term follow-up examination. Results There were no significant differences between the two groups regarding major (24 vs. 17%; p = 0.366) and minor surgical complications (61 vs. 70%; p = 0.318). However, the ALT group showed a significantly higher need for secondary surgeries (39 vs. 19%; p = 0.022). Sixty-eight patients (76%) returned for long-term follow-up evaluation (mean: 51.2 months, range: 13–71 months). The ALT group showed significantly less pain at the recipient (p = 0.0004) and donor (p = 0.010) sites, and scar assessment revealed significantly better results (p < 0.001). Additionally, the ALT group showed better depth (p = 0.017) and superficial (p = 0.007) sensation and enabled better shoe provision (p = 0.014). Conclusion Both the free ALT and gracilis flaps are well suited for plantar reconstruction, yielding overall similar functional outcomes. However, the ALT flap produces less scarring and pain, while showing better recovery of sensation and enabling better shoe provision. The ALT flap thus presents our preferred option.