The main topic of this paper is low‐cost public key cryptography in wireless sensor nodes. Security in embedded systems, for example, in sensor nodes based on field programmable gate array (FPGA), demands low cost but still efficient solutions. Sensor nodes are key elements in the Internet of Things paradigm, and their security is a crucial requirement for critical applications in sectors such as military, health, and industry. To address these security requirements under the restrictions imposed by the available computing resources of sensor nodes, this paper presents a low‐area FPGA‐prototyped hardware accelerator for scalar multiplication, the most costly operation in elliptic curve cryptography (ECC). This cryptoengine is provided as an enabler of robust cryptography for security services in the IoT, such as confidentiality and authentication. The compact property in the proposed hardware design is achieved by implementing a novel digit‐by‐digit computing approach applied at the finite field and curve level algorithms, in addition to hardware reusing, the use of embedded memory blocks in modern FPGAs, and a simpler control logic. Our hardware design targets elliptic curves defined over binary fields generated by trinomials, uses fewer area resources than other FPGA approaches, and is faster than software counterparts. Our ECC hardware accelerator was validated under a hardware/software codesign of the Diffie‐Hellman key exchange protocol (ECDH) deployed in the IoT MicroZed FPGA board. For a scalar multiplication in the sect233 curve, our design requires 1170 FPGA slices and completes the computation in 128820 clock cycles (at 135.31 MHz), with an efficiency of 0.209 kbps/slice. In the codesign, the ECDH protocol is executed in 4.1 ms, 17 times faster than a MIRACL software implementation running on the embedded processor Cortex A9 in the MicroZed. The FPGA‐based accelerator for binary ECC presented in this work is the one with the least amount of hardware resources compared to other FPGA designs in the literature.