Well-being and smartphone use are thought to influence each other. However, previous studies mainly focused on one direction (looking at the effects of smartphone use on well-being) and considered between-person effects, with self-reported measures of smartphone use. By using 2548 assessments of well-being and trace data of smartphone use collected for 45 consecutive days in 82 adolescent participants (M = 13.47, SD = 1.62, 54% females), the present study disentangled the reciprocal and individual dynamics of well-being and smartphone use. Hierarchical Bayesian Continuous Time Dynamic Models were used to estimate how a change in frequency and duration of smartphone use predicted a later change in well-being, and vice versa. Results revealed that (i) when participants used the smartphone frequently and for a longer period, they also reported higher levels of well-being; (ii) well-being positively predicted subsequent duration of smartphone use; (iii) usage patterns and system dynamics showed heterogeneity, with many subjects showing reciprocal effects close to zero; finally, (iv) changes in well-being tend to persist longer than changes in the frequency and duration of smartphone use.