Low back pain (LBP) is known to affect cyclists. This study aimed to describe perceived lumbar dysfunction and compare the pain sensation in recreational cyclists who practice road and mountain biking. Forty males were randomly assigned to carry out a 3-h road cycling (RC) and mountain biking (MTB) time trial (TT) at submaximal intensity. LBP and pain pressure threshold (PPT) were measured before and after the TT. A significant increment at the LBP was found after RC TT (p < 0.001; d = 2.61), similar to MTB TT (p < 0.001; d = 2.65). However, PPT decreased after completing the RC TT (p < 0.001; d = 1.73) and after MTB TT (p = 0.024; d = 0.77). There were no differences in the LBP evolution between both interventions (p > 0.01). Low back pain perception increases with cycling in recreational cyclists. Nevertheless, this increase appears to be more related to the traits of the cyclist than the modality practiced.