This study aimed at evaluating the impact of seasons on the nutritional status and on dietary cassava-related cyanide exposure in Burhinyi and Idjwi, two areas in the eastern Democratic Republic of the Congo, witnessing similarly high cassava-derived cyanide poisoning but differently affected by konzo and malnutrition. Cyanide content in cassava roots and flour, and urinary thiocyanate levels (uSCN) of 54 subjects (40 from Burhinyi and 14 from Idjwi, aged 28.7 (12.1) years, 63% women) were measured during the rainy season (RS) and dry season (DS), using picrate paper kits A and D1. Local processing methods proved to be efficient in removing cyanogenic compounds in fresh cassava roots during the RS. However, the cyanide content in flour samples significantly increased during DS, with ~50% of samples containing unsafe levels (>10 ppm) of cyanide content. Strikingly, the uSCN (µmol/L), from being comparably high in RS (~172.0), slightly decreased during DS in Burhinyi (~103.2; p = 0,3547), but not in Idjwi (~172; p = 0,1113). Furthermore, serum proteins and albumin levels significantly decreased during the DS, witnessing a worsening of nutritional status, in Burhinyi but not in Idjwi. The consumption of bitter cassava roots (OR = 5.43, p = 0.0144) and skipping heap fermentation (OR = 16.67, p = 0.0021) were independently associated with very high uSCN levels during the DS. Thus, restoring the traditional processing methods, and complying with them in either season should ensure the safe consumption of cassava.