Indonesia’s e-commerce development, with growth forecast of up to USD 300 billion by 2020, encourages many e-commerce companies to create new value in their products/services. Opportunities for e-commerce start-up collaboration programs increase the opportunities for e-commerce to grow. In e-commerce, decision-making for collaborations tends to be intuitive, centralized, and does not use strategic management tools. This study aims to identify critical factors as the main consideration in collaborative decision-making between e-commerce companies and partners. The study was conducted by developing a questionnaire for decision-makers in e-commerce collaborations. The study used the TOE framework, AHP, and TOPSIS methods. As part of the research’s object, the payment method was chosen for an e-commerce company collaborative program. Based on the criteria identified against the existing framework, there are 11 critical factors. The top three criteria are (1) networks and cooperation, (2) management commitment, and (3) knowledge and expertise in digital business. Based on the TOE framework, the main priority is the provision of e-wallet payment methods, which can be done by adding service providers. While research is limited as to the factors’ priority, future studies are suggested to select other collaborative programs or develop a collaborative strategy framework.