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Abstract Electrical impedance spectroscopy (EIS) is an electrical impedance technique to characterize the fruits and vegetables in terms of their frequency dependent bioimpedance profile. Standalone, portable, and low‐cost instrumentation is always preferred for conducting EIS procedures. This article reports the studies on the design and development of a Microcontroller based portable impedance measurement system to conduct the EIS studies on the fruits during ripening and storage. The proposed laboratory based EIS system is developed with a Microcontroller ATmega16, a Direct Digital Synthesizers based constant current source AD5930, a current to voltage converter, a low pass filter, and a DSO. To test and evaluate the developed system, the cucumber impedance is studied under the storage condition using EIS to characterize the cucumber freshness from the electrical impedance data. The real parts, imaginary parts of the cucumber impedance are calculated and the Nyquist diagrams are analyzed to study the equivalent circuit analysis. The developed system is compared with a standard impedance analyzer and it is observed that the results obtained from the developed system closely match with the data measured by the commercial impedance analyzer. The developed system is also found suitable for EIS studies of fruits, vegetables, and other biological tissues. The developed system is found low‐cost, fast, and user friendly. PCB based version of the proposed system with display unit will be found as a portable, standalone, and EIS system suitable for outdoor measurement in agricultural‐field applications. Practical applications Microcontroller based low cost electrical impedance spectroscopy (EIS) has been developed and is studied for EIS based fruit ripening analysis. The system is compared with the standard commercial impedance analyzer and it is found suitable fruit ripening characterization, vegetable freshness detection, and health studies of other biological tissues. The microcontroller based EIS system is found portable, low cost, fast, and user friendly device which can be used in laboratory, cultivation fields, cold storages and shops and markets. The developed system allows nontechnical person to operated and collect the data from fruit and vegetable samples. The system acquired data significantly correlate the bioimpedance variation with the ripening states which can be potentially utilized to study the fruit ripening noninvasively at low cost. Hence the product‐form of the developed devise could even be operated by field persons, farmers, and other common men to evaluate the fruit ripening and vegetable freshness.