In this work, a standard and unified method for monitoring hardware accelerators in Reconfigurable Computing Architectures is proposed, based on a standard software monitoring interface. The open source Performance Application Programming Interface (PAPI) library is commonly used in the field of High Performance Computing and aims at providing event information directly extracted from a set of Performance Monitor Counters. Important events such as data and instruction cache misses, hardware interrupts, etc. are collected to analyze and profile applications to pinpoint the contingent bottlenecks. In other words, it serves as a "Hardware Abstraction layer" for applications running in the user-space. In this paper, its use is extended by proposing a method to target custom Performance Hardware Registers on accelerators built upon an FPGA. Furthermore, portability and standardization are discussed and the overhead associated with PAPI use is evaluated. Two hardware examples are proposed to evaluate this approach: a simple counter and an infrastructure for hardware accelerators called ARTICo 3 .