Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of concern in raw milk dairy products. Ensuring product safety requires regular own-check testing, but evidence on naturally occurring STEC behavior during aging remains limited. This study analyzed three batches of bovine raw milk washed-rind cheese produced with STEC-positive curds to evaluate: (I) STEC distribution within cheese wheels and (II) STEC behavior during aging. STEC detection followed ISO/TS 13136:2012. First, two cheese wheels from batch A were sampled at the core (n = 4) and external (n = 4) locations at three timepoints (55, 85, and 150 days after production). External regions showed higher detection rates than the core, but this pattern was inconsistent, indicating heterogeneous STEC distribution. Second, batches B (n = 25) and C (n = 24) were sampled at four timepoints (85–86, 121–122, 170–171, and 197–198 days after production). In batch B, 16/25 wheels tested positive at least once, with alternating positive/negative patterns. In batch C, no wheel remained consistently negative, and only 2/24 wheels were negative at the final timepoint. These findings highlight the heterogeneous distribution and prolonged detectability of STEC in semi-cooked bovine raw milk cheese up to 198 days of aging, emphasizing the challenges associated with STEC sampling and detection in this product.