In rehabilitation, exercise instructions are multi-modal and can include a focus of increasing mean activity of a target muscle and inhibiting aberrant synergistic muscle activity, particularly during shoulder exercises, such as the prone horizontal abduction (PHA). The objective was to compare the immediate effects and short-term retention of multi-modal exercise instruction by a physical therapist written only instruction on normalized mean upper and lower trapezius muscle activity during three phases (concentric/isometric/eccentric) versus of an isotonic PHA exercise between participants with and without shoulder pain. Surface electromyography (EMG) was recorded from fourteen healthy participants and twelve participants with shoulder pain during the PHA exercise under two conditions: (1) written only instructions and (2) multi-modal instruction. Retention of multi-modal instruction on muscle activity was assessed one week later. Results demonstrate 12.8–16.0% increase in lower trapezius muscle activity during the concentric and isometric phases with multi-modal instructions in both groups. Inhibition of the upper trapezius did not occur in either group. Facilitation effects were maintained in short-term follow-up. Findings suggest that regardless of shoulder pain, multi-modal instruction by a physical therapist facilitates greater neuromuscular activity of a targeted muscle compared to written instructions alone and these effects are retained.