Background <p>Flexible pes planus (FPP) is associated with altered foot biomechanics, reduced ankle dorsiflexion, and impaired neuromuscular function, which may affect balance and performance. Manual therapy targeting joint and soft tissue structures is commonly used; however, the comparative immediate effects of these approaches remain unclear.</p> Aims <p>To compare the immediate effects of joint-oriented manual therapy (J-MT) and soft-tissue–oriented manual therapy (ST-MT) on dorsiflexion range of motion (DFROM), foot morphology, dynamic balance, and muscle mechanical properties in physically active adults with FPP.</p> Methods <p>In this prospective randomized controlled trial, 45 adults (18–35&#xa0;years) with FPP were allocated to J-MT (<i>n</i> = 15), ST-MT (<i>n</i> = 15), or control (<i>n</i> = 15) using concealed block randomization. J-MT involved ankle–foot joint mobilization, while ST-MT targeted the triceps surae, Achilles tendon, and plantar fascia. Controls received no intervention. The primary outcome was DFROM (weight-bearing lunge test). Secondary outcomes included navicular drop (ND), Foot Posture Index (FPI), Y-Balance Test, and myotonometric muscle properties. Assessments were performed pre- and post-intervention.</p> Results <p>Both J-MT and ST-MT significantly reduced ND and FPI versus controls (<i>p</i> &lt; 0.05), with no between-group difference. J-MT improved DFROM and anterior reach more than ST-MT (<i>p</i> &lt; 0.05). No significant differences in dynamic balance were observed. ST-MT reduced soleus tone and tibialis anterior stiffness, while both interventions improved soleus elasticity (<i>p</i> &lt; 0.05). No adverse events occurred.</p> Conclusions <p>J-MT and ST-MT produce immediate, parameter-specific effects in FPP. J-MT enhances dorsiflexion, whereas ST-MT better modulates muscle mechanical properties, supporting the selection of targeted interventions.</p>