Technical Debt (TD) is a software engineering metaphor that resembles the production of poor-quality code to going into debt. In particular, a development team that “saves” effort while developing by not removing inefficiencies, has to “pay-back” with interest, in the form of additional maintenance costs (i.e., fixing bugs, adding features, etc.) due to the poor maintainability of the developed code. Although maintainability assurance is an established practice in traditional software development (lately known as TD management), it has still not attracted the attention of scientific software developers; i.e., researchers writing code and developing tools for purely research purposes. Nevertheless, based on the literature and practice, maintainability seems to be ranked as an important key-driver for the development of such applications; since the effort needed to update the code before the experimentation (e.g., executing a simulation) is common and should not receive low priority. In this paper, we present the outcome of a 3-year research project on Technical Debt Management (TDM) for scientific software development. The outcome of the project is a framework (termed: EXA2PRO TDM framework) and an accompanying platform for assisting scientific software developers in managing the TD of their applications. The framework is a collection of methods tailored for the mainstream programming languages of scientific software development, which have been empirically validated through five pilot applications. The majority of the EXA2PRO framework suggestions have been applied by scientific software developers and eased future maintenance activities.