Significant progress has been made over the last decades in understanding the physiological and neural bases of cognitive processes and behavior. The advent of new and improved brain imaging tools, that allow monitoring brain activity in natural environments, is expected to provide a complementary perspective into the relationship of neurophysiological markers. Functional near infrared spectroscopy (fNIRS), an emerging brain monitoring technology that relies on optical techniques to detect changes of cortical hemodynamic responses to sensory, motor, or cognitive activation is an ideal candidate tool. Consistent with the neuroergonomic approach, ultra-portable and wireless fNIRS sensors can allow capturing brain at work in naturalistic environments during complex tasks. This presentation will discuss emerging trends for fNIRS applications from aerospace to medicine, with diverse populations and towards clinical life-saving solutions. We will review recent projects such as mental workload assessment of special operators performing standardized and complex cognitive tasks and development of expertise during practice of complex cognitive and visuomotor tasks (ranging from aircraft piloting, robot control to surgical tool use). Various recent synergistic fNIRS applications that put the brain in the loop for human-human and human-machine interaction will be discussed including synthetic speech perception, interpersonal neural synchronization and brain computer interfaces.