In this work we present the performance of a fast acquisition system for in-beam PET monitoring during the irradiation of a PMMA phantom with a clinical proton beam. The experimental set-up was based on 4 independent detection modules. Two detection modules were placed at one side of a PMMA phantom and the other two modules were placed at the opposite side of the phantom. One detection module was composed of a Silicon Photon Multiplier produced by AdvanSiD coupled to a single scintillating LYSO crystal. The read-out system was based on the TOFPET ASIC managed by a Xilinx ML605 FPGA Evaluation Board (Virtex 6). The irradiation of the PMMA phantom was performed at the CNAO hadrontherapy facility (Pavia, Italy) with a 95 MeV pulsed proton beam. The pulsed time structure of the proton beam was reconstructed by each detection module. The β+ annihilation peak was successfully measured and the production of β+ isotopes emitters was observed as increasing number of 511 keV events detected during irradiation. Finally, after the irradiation, the half lives of the 11C and 15O radioactive isotopes were estimated.