Sally Lightfoot crabs (Grapsus grapsus), brightly colored coastal scavengers, are widespread across the Galapagos Islands and along the western coasts of South and Central America. This study evaluated microplastic (MP) pollution in native Sally Lightfoot crabs from three locations on San Cristobal Island (La Loberia, Puerto Tablas, and Punta Carola) in the Galapagos Archipelago. We analyzed the blood chemistry and basic health parameters and presence of MPs in the gills (GILL) and gastrointestinal tract (GIT) of 60 crabs (20 per location), employing Fourier Transform Infrared Spectroscopy (FT-IR) for MP quantification. Fibers constituted the most common polymer type (n = 106), followed by fragments (n = 27) and films (n = 5). A Generalized Linear Model (GLM) analysis assessed the relationships between microplastic presence in the gills and gastrointestinal tract and variables such as sex, weight, length, location, and heart rate. The best-fitting model (AICc = 149.27) included only the intercept, indicating no significant associations between MP presence in gills/GIT and the tested variables. A Chi-Squared test showed no significant differences across locations in terms of MP shape, type, color, length, or polymer composition, suggesting uniform MP properties across sites, likely due to similar pollution sources or transport patterns. However, a Kruskal-Wallis rank sum test revealed a significant difference in MP accumulation between the gastrointestinal tract and gill tissues (chi-squared = 12.534, df = 1, p = 0.0004), indicating differential MP retention in these tissues.