Fluopyram and trifloxystrobin are widely used for controlling various plant diseases in cucumbers and cowpeas. However, data on residue behaviors in plant cultivation and food processing are currently lacking. Our results showed that cowpeas had higher fluopyram and trifloxystrobin residues (16.48–247.65 μg/kg) than cucumbers (877.37–3576.15 μg/kg). Moreover, fluopyram and trifloxystrobin dissipated faster in cucumbers (half-life range, 2.60–10.66 d) than in cowpeas (10.83–22.36 d). Fluopyram and trifloxystrobin were the main compounds found in field samples, and their metabolites, fluopyram benzamide and trifloxystrobin acid, fluctuated at low residue levels (≤76.17 μg/kg). Repeated spraying resulted in the accumulation of fluopyram, trifloxystrobin, fluopyram benzamide and trifloxystrobin acid in cucumbers and cowpeas. Peeling, washing, stir-frying, boiling and pickling were able to partially or substantially remove fluopyram and trifloxystrobin residues from raw cucumbers and cowpeas (processing factor range, 0.12–0.97); on the contrary, trifloxystrobin acid residues appeared to be concentrated in pickled cucumbers and cowpeas (processing factor range, 1.35–5.41). Chronic and acute risk assessments suggest that the levels of fluopyram and trifloxystrobin in cucumbers and cowpeas were within a safe range based on the field residue data of the present study. The potential hazards of fluopyram and trifloxystrobin should be continuously assessed for their high residue concentrations and potential accumulation effects.