Context. Much attention has been placed on the dust distribution in protostellar envelopes, but there are still many unanswered questions regarding the physico-chemical structure of the gas. Aims. Our aim is to start identifying the factors that determine the chemical structure of protostellar regions, by studying and comparing low-mass embedded systems in key molecular tracers. Methods. The cold and warm chemical structures of two embedded Class 0 systems, IRAS 16293−2422 and VLA 1623−2417 were characterized through interferometric observations. DCO⁺, N₂H⁺, and N₂D⁺ were used to trace the spatial distribution and physics of the cold regions of the envelope, while c-C₃H₂ and C₂H from models of the chemistry are expected to trace the warm (UV-irradiated) regions. Results. The two sources show a number of striking similarities and differences. DCO⁺ consistently traces the cold material at the disk-envelope interface, where gas and dust temperatures are lowered due to disk shadowing. N₂H⁺ and N₂D⁺, also tracing cold gas, show low abundances toward VLA 1623−2417, but for IRAS 16293−2422, the distribution of N₂D⁺ is consistent with the same chemical models that reproduce DCO⁺. The two systems show different spatial distributions c-C₃H₂ and C₂H. For IRAS 16293−2422, c-C₃H₂ traces the outflow cavity wall, while C₂H is found in the envelope material but not the outflow cavity wall. In contrast, toward VLA 1623−2417 both molecules trace the outflow cavity wall. Finally, hot core molecules are abundantly observed toward IRAS 16293−2422 but not toward VLA 1623−2417. Conclusions. We identify temperature as one of the key factors in determining the chemical structure of protostars as seen in gaseous molecules. More luminous protostars, such as IRAS 16293−2422, will have chemical complexity out to larger distances than colder protostars, such as VLA 1623−2417. Additionally, disks in the embedded phase have a crucial role in controlling both the gas and dust temperature of the envelope, and consequently the chemical structure.