Purpose Human skeletal muscle has the profound ability to hypertrophy in response to resistance training (RT). However, this has a high energy and protein cost and is presumably mainly restricted to recruited muscles. It remains largely unknown what happens with nonrecruited muscles during RT. This study investigated the volume changes of 17 recruited and 13 nonrecruited muscles during a 10-wk single-joint RT program targeting upper arm and upper leg musculature. Methods Muscle volume changes were measured by manual or automatic 3D segmentation in 21 RT novices. Subjects ate ad libitum during the study and energy and protein intake were assessed by self-reported diaries. Results Posttraining, all recruited muscles increased in volume (range: +2.2% to +17.7%, P < 0.05), whereas the nonrecruited adductor magnus (mean: -1.5% ± 3.1%, P = 0.038) and soleus (-2.4% ± 2.3%, P = 0.0004) decreased in volume. Net muscle growth (r = 0.453, P = 0.045) and changes in adductor magnus volume (r = 0.450, P = 0.047) were positively associated with protein intake. Changes in total nonrecruited muscle volume (r = 0.469, P = 0.037), adductor magnus (r = 0.640, P = 0.002), adductor longus (r = 0.465, P = 0.039), and soleus muscle volume (r = 0.481, P = 0.032) were positively related to energy intake. When subjects were divided into a HIGH or LOW energy intake group, overall nonrecruited muscle volume (-1.7% ± 2.0%), adductor longus (-5.6% ± 3.7%), adductor magnus (-2.8% ± 2.4%), and soleus volume (-3.7% ± 1.8%) decreased significantly (P < 0.05) in the LOW but not the HIGH group. Conclusions To our knowledge, this is the first study documenting that some nonrecruited muscles significantly atrophy during a period of RT. Our data therefore suggest muscle mass reallocation, that is, that hypertrophy in recruited muscles takes place at the expense of atrophy in nonrecruited muscles, especially when energy and protein availability are limited.