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Objectives To develop and evaluate a standardised, fully automated assessment procedure for patient treatment preferences suitable for use in randomised controlled trials (RCTs) with remote or digital health interventions.Design Multiphase developmental study followed by implementation in a fully randomised preference trial (FRPT).Setting University and outpatient cancer care settings in Switzerland; implementation in RCTs with a remote digital health intervention.Participants 50 medical students for pilot testing; 11 patients with cancer for qualitative testing; 124 adult patients with cancer experiencing fatigue or sleep problems in an FRPT with a remote digital health intervention.Primary and secondary outcome measures Primary outcome: feasibility and applicability of a standardised digital preference assessment procedure. Secondary outcomes: distribution and strength of treatment preferences, reasons for preference.Results A procedure with three items for assessing treatment preferences was developed and refined based on pilot testing, stakeholder meetings and patient interviews. The stepwise procedure ensured that study participants with an initially unclear preference were finally able to report their preference. The majority of students (91.7%) indicated their preference already in the first assessment step. Similar in the RCT phase, 110 of 124 participants (88.7%) indicated their preference in the first step. Preference drivers included interest, perceived ease and conceptual appeal in addition to expected treatment benefits.Conclusions Our fully automated standardised preference assessment with three items appears feasible in trials with digital health interventions. Future trials with two active treatment conditions should consider implementation of such a preference assessment to evaluate non-specific treatment effects driven by the match of patients’ preferences with the respective treatment.Trial registration numbers DRKS00035596; DRKS00035541; SNCTP000006209.