We aimed to investigate whether muscle fiber cross‐sectional area (fCSA) and associated molecular processes could be differently affected at the group and individual level by manipulating resistance training (RT) variables. Twenty resistance‐trained subjects had each leg randomly allocated to either a standard RT (RT‐CON: without specific variables manipulations) or a variable RT (RT‐VAR: manipulation of load, volume, muscle action, and rest interval at each RT session). Muscle fCSA, satellite cell (SC) pool, myonuclei content, and gene expression were assessed before and after training (chronic effect). Gene expression was assessed 24 h after the last training session (acute effect). RT‐CON and RT‐VAR increased fCSA and myonuclei domain in type I and II fibers after training (p < 0.05). SC and myonuclei content did not change for both conditions (p > 0.05). Pax‐7, MyoD, MMP‐2 and COL3A1 (chronic) and MGF, Pax‐7, and MMP‐9 (acute) increased similar for RT‐CON and RT‐VAR (p < 0.05). The increase in acute MyoG expression was significantly higher for the RT‐VAR than RT‐CON (p < 0.05). We found significant correlation between RT‐CON and RT‐VAR for the fCSA changes (r = 0.89). fCSA changes were also correlated to satellite cells (r = 0.42) and myonuclei (r = 0.50) changes. Heatmap analyses showed coupled changes in fCSA, SC, and myonuclei responses at the individual level, regardless of the RT protocol. The high between and low within‐subject variability regardless of RT protocol suggests that the intrinsic biological factors seem to be more important to explain the magnitude of fCSA gains in resistance‐trained subjects.