The expanding blue economy, marked by its focus on sustainable use of ocean resources, offers enormous opportunity for Small and Medium-sized Enterprises (SMEs). However, for SMEs to properly integrate and succeed in this economy, they must first have a thorough awareness of the sector’s challenges and prospects. This research used a scoping review and a qualitative study to identify the challenges and opportunities facing SMEs operating in the blue economy. The study discovered recurring themes and gaps in the existing literature by conducting an extensive examination of scholarly publications. The key challenges identified include complicated regulatory frameworks, restricted access to funding, infrastructure restrictions, talent deficiencies, government support, and market outreach. In-depth interviews with Malaysian SME leaders, industry stakeholders, and policymakers were conducted to decipher these findings. The results of interviews confirmed the relevance of the regulatory framework, infrastructure restrictions, talent deficit, and market access challenges in the Malaysian context. In particular, the study revealed emerging opportunities for Malaysian blue SMEs in sectors such as renewable energy, sustainable fisheries, marine biotechnology, and ecotourism. The study emphasizes the importance of an encouraging policy framework, knowledge-sharing platforms, and capacity building activities. It finishes by underlining the ability of SMEs to drive a sustainable and thriving blue economy, if challenges are systematically handled, and opportunities are appropriately capitalized.