The last decade can be confidently described as turbulent for the economy of the Russian Federation. The global COVID-19 pandemic, followed by an increase in the budget’s expenditure side and its structural transformation due to foreign policy events, would have been a shock for any economy in the world. However, the events that unfolded have led to the situation where, interpreting resilience as being close in meaning to elasticity, we can confidently assert that the economy of the Russian Federation is one of the most resilient in the world. Under these conditions, the ability of organizations and enterprises to take advantage of local crisis points to enhance their capabilities becomes especially valuable. One of the most affected sectors, which required unconventional and prompt solutions, was the civil aviation industry, which is of particular importance to our country. At the same time, one of the key tools for the innovative development of any companies in the modern world is digital transformation and the widespread implementation of digital solutions. The aim of the study was to summarize information in the field of process innovations and examine their features in relation to the digital transformation of an individual enterprise, using the example of the civil air transportation industry, and to propose new effective tools for assessing process innovations, taking into account their specific characteristics. The study was carried out using a comprehensive approach based on methods for collecting, analyzing, and visualizing data within the framework of a scientific approach in several stages. As a result, at the first stage of the study, based on an analysis of the works of domestic and foreign scholars, the specific features of process innovations characteristic of civilian airlines were formulated, and the main directions for their implementation were also identified. At the second stage, a mechanism for implementing a development program based on process innovations in civil airlines was proposed, along with algorithms for assessing their potential and feasibility. At the third stage, based on the research conducted, these algorithms were tested using the example of S7 Airlines’ digital transformation program.