The objective of this study is to clarify the functional roles of upper limb muscles during standing and seated cycling when power output increases. We investigated the activity of seven upper limb and trunk muscles using surface electromyography (EMG). Power outputs ranged from ~100–700 W with a pedalling frequency of 90 revolution per minute. Three-dimensional handle and pedal forces were simultaneously recorded. Using non-negative matrix factorisation, we extracted muscle synergies and we analysed the integrated EMG and EMG temporal patterns. Most of the muscles showed tonic activity that became more phasic as power output increased. Three muscle synergies were identified, associated with (i) torso stabilisation, (ii) compensation/generation of trunk accelerations and (iii) upper body weight support. Synergies were similar for seated and standing positions (Pearson’s r > 0.7), but synergy #2 (biceps brachii, deltoidus and brachioradialis) was shifted forward during the cycle (~7% of cycle). The activity levels of synergy #1 (latissimus dorsi and erector spinae) and synergy #2 increased markedly above ~500 W (i.e., ~+40–70% and +130–190%) and during periods corresponding to ipsi- and contralateral downstrokes, respectively. Our study results suggest that the upper limb and trunk muscles may play important roles in cycling when high power outputs are required.