Eccentric quasi-isometric (EQI) contractions combine isometric holding with subsequent eccentric (ECC) lengthening. Although EQI exercise has gained attention, its chronic effects remain unclear. This study compared morphological and functional adaptations to EQI and ECC resistance exercise. Forty-eight healthy, regularly trained adult participants were randomly allocated (sex-stratified) to EQI, ECC, or control groups (n = 16 per group; age 22.91 ± 4.70). The intervention groups completed a six-week training program with matched load and time under tension. Outcomes assessed pre- and post-intervention included Achilles tendon properties, gastrocnemius architecture, ankle range of motion, and plantar flexor strength. Both EQI and ECC training increased Achilles tendon thickness, gastrocnemius fascicle length and muscle thickness, and lateral gastrocnemius pennation angle compared to control (all p ≤ 0.001; η² = 0.53-0.79), with no differences between protocols (p = 0.227-0.965). Ankle dorsiflexion (open and closed kinetic chain) and concentric, ECC, and isometric strength improved in both intervention groups compared to control (p ≤ 0.019; η² = 0.33-0.77), without between-group differences (p = 0.561-0.976). Only ECC training increased EQI time under tension and torque impulse (p = 0.012-0.020), while tendon stiffness, medial gastrocnemius pennation angle, and EQI angular velocity did not change (p ≥ 0.065). EQI and ECC training produced comparable improvements in muscle–tendon morphology, strength, and ankle dorsiflexion when load and time under tension were matched, while EQI training was associated with lower muscle soreness.