This study aimed to assess microplastics (MPs) in the digestive glands of Mytilus galloprovincialis mussels. Mussels were collected from pristine, aquaculture, and port areas of the northern Adriatic Sea (Slovenia and Croatia coastline). MPs were detected using scanning electron microscopy (SEM) and energy dispersive spectrometry (EDS). The characterized MPs were further categorized based on their shape, size, and color. The highest number of 32.85 ± 27.98 MPs per mussel digestive gland was found in the mussels sampled from the ACI marina Rovinj (Croatia). The predominant MPs found in the mussel digestive glands at all investigated locations belonged to the smallest analyzed category (5–10 μm in size) and exhibited spherical and fragment shapes. The most abundant MPs found in mussels by color were white particles. MPs were found in both wild and farmed mussels and, hence, the results point out that the abundance of microplastic pollution is omnipresent along the coastal waters of the northern Adriatic Sea.