Background Insufficient physical activity is a public health concern. New technologies may improve physical activity levels and enable the identification of its predictors with high accuracy. The Precious smartphone app was developed to investigate the effect of specific modular intervention elements on physical activity and examine theory-based predictors within individuals. Objective This study pilot-tested a fully automated factorial N-of-1 randomized controlled trial (RCT) with the Precious app and examined whether digitalized motivational interviewing (dMI) and heart rate variability–based biofeedback features increased objectively recorded steps. The secondary aim was to assess whether daily self-efficacy and motivation predicted within-person variability in daily steps. Methods In total, 15 adults recruited from newspaper advertisements participated in a 40-day factorial N-of-1 RCT. They installed 2 study apps on their phones: one to receive intervention elements and one to collect ecological momentary assessment (EMA) data on self-efficacy, motivation, perceived barriers, pain, and illness. Steps were tracked using Xiaomi Mi Band activity bracelets. The factorial design included seven 2-day biofeedback interventions with a Firstbeat Bodyguard 2 (Firstbeat Technologies Ltd) heart rate variability sensor, seven 2-day dMI interventions, a wash-out day after each intervention, and 11 control days. EMA questions were sent twice per day. The effects of self-efficacy, motivation, and the interventions on subsequent steps were analyzed using within-person dynamic regression models and aggregated data using longitudinal multilevel modeling (level 1: daily observations; level 2: participants). The analyses were adjusted for covariates (ie, within- and between-person perceived barriers, pain or illness, time trends, and recurring events). Results All participants completed the study, and adherence to activity bracelets and EMA measurements was high. The implementation of the factorial design was successful, with the dMI features used, on average, 5.1 (SD 1.0) times of the 7 available interventions. Biofeedback interventions were used, on average, 5.7 (SD 1.4) times out of 7, although 3 participants used this feature a day later than suggested and 1 did not use it at all. Neither within- nor between-person analyses revealed significant intervention effects on step counts. Self-efficacy predicted steps in 27% (4/15) of the participants. Motivation predicted steps in 20% (3/15) of the participants. Aggregated data showed significant group-level effects of day-level self-efficacy (B=0.462; P<.001), motivation (B=0.390; P<.001), and pain or illness (B=−1524; P<.001) on daily steps. Conclusions The automated factorial N-of-1 trial with the Precious app was mostly feasible and acceptable, especially the automated delivery of the dMI components, whereas self-conducted biofeedback measurements were more difficult to time correctly. The findings suggest that changes in self-efficacy and motivation may have same-day effects on physical activity, but the effects vary across individuals. This study provides recommendations based on the lessons learned on the implementation of factorial N-of-1 RCTs.