The Arduino prototyping hardware platform has a large following of educators and robotics hobbyists around the world. Each Arduino board has the I/O sockets in a fixed position therefore allowing it to be extended with a variety of custom daughter-boards (called Shields).

Flowol 4+ supports the Arduino Uno, Arduino Leonardo and the Arduino Duemilanove (with either the ATmega328p or 168 microcontrollers). There are also many Arduino-compatible boards made by other companies (e.g. Freeduino and DFRobot boards). Flowol supports many compatible boards with a 16MHz resonator.

The flowchart can be run in Flowol while the Arduino board is connected (online mode). Flowol can also compile and download the flowchart to be run remotely on the Arduino. Flowol flowcharts can contain multiple Start symbols which run in parallel. Flowol 4 can download programs with several parallel flowcharts to run remotely on the Arduino

Flowol supports a variety of digital/analog I/O devices with the Arduino. In particular, pins 4/5 and 6/7 can be configured to support bi-directional motors. Flowol also supports servos, PWM outputs, digital encoders (on pins 2 and 3), ultrasonic distance sensor (HC-SR04 type), LCD displays and Serial communication.