In-shell pecans are typically harvested after falling from trees to the ground, presenting a potential route of contamination of foodborne pathogens from soil contact. In-shell pecans are often subjected to various processing or washing steps prior to being shelled. This study determined Shiga toxin-producing Escherichia coli (STEC) reductions after treatment with antimicrobial washes on direct and soil-inoculated in-shell pecans and evaluated the cross-contamination potential of the spent pecan washes after treatment. Pecans were directly and soil-inoculated with an STEC cocktail (O157:H7, O157:NM, O121, O26). Direct inoculation was achieved by spraying the STEC cocktail on the pecans. For soil-inoculation pecans, autoclaved soil was sprayed with the STEC cocktail, homogenized for 2 min, and used to coat in-shell pecans. Inoculated pecans were washed in treatments of 2% lactic acid (LA), 1,000 ppm free chlorine (sodium hypochlorite; NaClO), hot water (HW; 85 ± 2 °C), or ambient water (C [control]; 18 ± 2 °C) for 2, 5, and 10 min and diluted to enumerate STEC populations. After treatments, 100 mL of the spent wash was vacuum filtered through a 0.45-µm membrane and plated on selective agar. HW significantly reduced STEC populations from pecans with and without soil regardless of treatment time (p < 0.05), NaClO reduced STEC populations more than the ambient control wash on directly inoculated pecans, but there were no significant differences between STEC reductions from ambient water (C), LA, and NaClO treatments on soil-inoculated pecans (p > 0.05). Larger STEC populations were enumerated from ambient water wash compared to the antimicrobial washes (p < 0.05). The HW, LA, and NaClO treatments were effective at maintaining the quality of the wash water, with STEC levels being generally at or below the detection limit (<1 CFU/100 mL), while HW was the most effective at reducing STEC from in-shell pecans with and without a soil coating (>5-log CFU/mL reductions).