Objective Although fly‐in‐fly‐out (FIFO) work practices are widely used, little is known about their impact on the motivation and wellbeing of FIFO workers across the course of their work cycles. Drawing from the job demands‐resources model, we aimed to test for the within‐person effects of time of work cycle, job demands, and job resources on emotional exhaustion and employee engagement at 3‐day intervals. Method A total of 52 FIFO workers filled out three or more online diary surveys after every 3 days of their on‐site work roster. The survey consisted of items drawn from previously validated scales. Bayesian hierarchical modelling of the day‐level data was conducted. Results Workers, on average, showed a decline in engagement and supervisor support, and an increase in emotional demand over the course of the work cycle. The results of the hierarchical modelling showed that day‐level autonomy predicted day‐level engagement and that day‐level workload and emotional demands predicted emotional exhaustion. Conclusions The findings highlight the importance of managing FIFO employees’ day‐to‐day experiences of job demands and job resources because of their influence on employee engagement and emotional exhaustion. To best protect FIFO worker day‐level wellbeing, employing organisations should ensure optimal levels of job autonomy, workload, and emotional demands. Practical implications, study limitations and areas for future research are outlined.