Background Prevention in psychiatry provides a promising way to address the burden of mental illness. However, established approaches focus on specific diagnoses and do not address the heterogeneity and manifold potential outcomes of help-seeking populations that present at early recognition services. Conceptualizing the psychopathology manifested in help-seeking populations from a network perspective of interacting symptoms allows transdiagnostic investigations beyond binary disease categories. Furthermore, modern technologies such as smartphones facilitate the application of the Experience Sampling Method (ESM). Objective This study is a combination of ESM with network analyses to provide valid insights beyond the established assessment instruments in a help-seeking population. Methods We will examine 75 individuals (aged 18-40 years) of the help-seeking population of the Cologne early recognition center. For a maximally naturalistic sample, only minimal exclusion criteria will be applied. We will collect data for 14 days using a mobile app to assess 10 transdiagnostic symptoms (ie, depressive, anxious, and psychotic symptoms) as well as distress level 5 times a day. With these data, we will generate average group-level symptom networks and personalized symptom networks using a 2-step multilevel vector autoregressive model. Additionally, we will explore associations between symptom networks and sociodemographic, risk, and resilience factors, as well as psychosocial functioning. Results The protocol was designed in February 2020 and approved by the Ethics Committee of the University Hospital Cologne in October 2020. The protocol was reviewed and funded by the Köln Fortune program in September 2020. Data collection began in November 2020 and was completed in November 2021. Of the 258 participants who were screened, 93 (36%) fulfilled the inclusion criteria and were willing to participate in the study. Of these 93 participants, 86 (92%) completed the study. The first results are expected to be published in 2022. Conclusions This study will provide insights about the feasibility and utility of the ESM in a help-seeking population of an early recognition center. Providing the first explorative phenotyping of transdiagnostic psychopathology in this population, our study will contribute to the innovation of early recognition in psychiatry. The results will help pave the way for prevention and targeted early intervention in a broader patient group, and thus, enable greater intended effects in alleviating the burden of psychiatric disorders. International Registered Report Identifier (IRRID) DERR1-10.2196/35206