A low-cost customized automated fertigation system for closed soilless culture under protected cultivation was developed; the hardware includes a programmable logic controller (PLC), a touch panel (HMI), and multichannel sensors. The controller unit was used to automate the whole fertigation process from preparing the fresh nutrient solution, its application in the field, and reuse of the drained nutrient solution (leachate) by balancing the nutrient with the addition of freshly prepared nutrient solution. The performance of the developed system was evaluated for cucumber cultivation with three fertigation levels (T1- 100 % fresh nutrient solution, T2- 90 % fresh nutrient solution with 10 % leachate, and T3- 80 % fresh nutrient solution with 20 % leachate) and three growing media (S1-cocopeat + cocochips v/v 1:1; S2- cocopeat + cocochips v/v 7:3 and S3- cocopeat) with three replications. Our findings showed crop yield (3.3–3.7 kg plant−1), total soluble solids (3.3–4.3 Brixo), total phenolic contents (0.81–0.88 mg/100 g), firmness (30.6–33.5 N) and antioxidant capacity (22.3–23.6 %). The highest yield was recorded under substrate S2 i.e. 3.7 kg plant−1 followed by under substrate S3 (3.4 kg plant−1) and S1 (3.3 kg plant−1) which may be attributed to better physical properties (low bulk density, high water retention capacity and high porosity) that enhanced the aeration and drainage in the media. However, there was no statistically significant difference found in the yield for the fertigation treatments which showed that we can successfully use 100 % of the leachate. Overall, the fruit yield and water use efficiency of cucumber crop fertigated with the automated system was found about 25–30 % and 50 % respectively higher as compared to the conventional fertigation system. In addition, the proposed system was found efficient in preparing and supplying fresh nutrient solution and reusing the drained nutrient solution after making the solution balance and disease-free.