The negative effects of phosphate (Pi) and/or nitrate (NO3−) fertilizers on the environment have raised an urgent need to develop crop varieties with higher Pi and/or nitrogen use efficiencies for cultivation in low‐fertility soils. Achieving this goal depends upon research that focuses on the identification of genes involved in plant responses to Pi and/or NO3− starvation. Although plant responses to individual deficiency in either Pi (–Pi/+NO3−) or NO3− (+Pi/–NO3−) have been separately studied, our understanding of plant responses to combined Pi and NO3− deficiency (–Pi/–NO3−) is still very limited. Using RNA‐sequencing approach, transcriptome changes in the roots and leaves of chickpea cultivated under –Pi/+NO3−, +Pi/–NO3− or –Pi/–NO3− conditions were investigated in a comparative manner. –Pi/–NO3− treatment displayed lesser effect on expression changes of genes related to Pi or NO3− transport, signalling networks, lipid remodelling, nitrogen and Pi scavenging/remobilization/recycling, carbon metabolism and hormone metabolism than –Pi/+NO3− or +Pi/–NO3− treatments. Therefore, the plant response to –Pi/–NO3− is not simply an additive result of plant responses to –Pi/+NO3− and +Pi/–NO3− treatments. Our results indicate that nutrient imbalance is a stronger stimulus for molecular reprogramming than an overall deficiency. Comparative transcriptome analyses revealed that combined phosphate (Pi) and nitrate (NO3−) deficiency had lower effects on expression changes of many Pi starvation‐responsive genes and NO3− starvation‐responsive genes than individual Pi and NO3− deficiencies did in chickpea plants.