The relevance of the study stems from the evolving nature of social objects and the increasing complexity of their structures and environmental interactions. Additionally, changing respondent attitudes to psychologists’ work necessitates advances in our methodological toolkit. Drawing on V. A. Mazilov’s principle that fi eld researchers should develop methods using a “bottom-up approach,” the study addresses the issues of four levels of methodology and advocates the use of “methodological bundles” (including system triads, vectors, continua, and “cross-cutting” concepts), to harmonize research and development (R&D) and scientifi c and practical work (NPR), integrating them into the disciplinary factual framework. The study aims to provide a historical and theoretical analysis of methodological and organizational aspects of R&D in modern organizations. Methods (tools): involved scientifi c literature analysis, subject-categorical analysis, and refl ection on practical and scientifi c experience in modern organizations. Results: it is shown that: 1) “methodological bundles” enable simplifi cation of reality fragments, reducing complex phenomena to predictable relationships; 2) their simplicity and clarity aids identifi cation of key scientifi c observations and gaps, supporting research continuity across generations; 3) these “bundles” indicate a common or unifi ed ontology of the studied phenomena; 4) although they do not always reconstruct ontologies fully, they reveal possible relationships and properties among reality fragments. Main conclusions: amid accelerating disciplinary development, diff erentiation into fi elds and scientifi c schools, narrowing of disciplinary approaches, and knowledge fragmentation, integrative methodological tools are as crucial as the discovery of new phenomena. Practical significance: such tools facilitate integration of diverse scientifi c knowledge fragments, fostering more constructive R&D in modern organizations.