We examined the effects of whey versus collagen protein on skeletal muscle cell signalling responses associated with mitochondrial biogenesis and protein synthesis in recovery from an acute training session completed with low carbohydrate (CHO) availability. In a repeated measures design (after adhering to a 36-h exercise-dietary intervention to standardise pre-exercise muscle glycogen), eight males completed a 75-min non-exhaustive cycling protocol and consumed 22 g of a hydrolysed collagen blend (COLLAGEN) or whey (WHEY) protein 45 min prior to exercise, 22 g during exercise and 22 g immediately post-exercise. Exercise decreased (P<0.05) muscle glycogen content by comparable levels from pre-to post-exercise in both trials (≈ 300 to 150 mmol.kg-1 dw). WHEY protein induced greater increases in plasma BCAAs (P=0.03) and leucine (P=0.02) than COLLAGEN. Exercise induced (P<0.05) similar increases in PGC-1α (5-fold) mRNA at 1.5 h post-exercise between conditions though no affect of exercise (P>0.05) was observed for p53, Parkin and Beclin1 mRNA. Exercise suppressed (P<0.05) p70S6K1 activity in both conditions immediately post-exercise (≈ 25 fmol.min-1.mg-1). Post-exercise feeding increased p70S6K1 activity at 1.5 h post-exercise (P<0.05), the magnitude of which was greater (P <0.05) in WHEY (180 ± 105 fmol.min-1.mg-1) versus COLLAGEN (73 ± 42 fmol.min-1.mg-1). We conclude that protein composition does not modulate markers of mitochondrial biogenesis when in recovery from a training session deliberately completed with low CHO availability. In contrast, whey protein augments post-exercise p70S6K activity compared with hydrolysed collagen, as likely mediated via increased leucine availability.