Field Programmable Gate Arrays (FPGAs) are used more and more frequently to implement cryptographic systems, which need random number generators (RNGs) to be embedded in the same device. The main challenge related to the implementation of a generator running inside FPGAs is that the physical source of randomness, such as jittered clock generator, is implemented in the configurable logic area, i.e. in the close vicinity of noisy running algorithms, which can have significant impact on generated numbers or even serve to attack the generator. A possible approach to prevent such influence is the use of Phase-Lock Loops (PLLs), which are separated from the re-configurable logic area inside the FPGA chip. In this paper, we propose a new architecture of the PLL-based TRNG including a method to avoid correlation in the output through control of timing in the sampling process, as well as new embedded tests based on the enhanced stochastic model. We also propose a workflow to help find the best parameters, such as output bitrate and entropy rate. We show that bitrates of around 400 kb/s or more can be achieved, while guaranteeing min-entropy rates per bit higher than 0.98 as required by the latest security standards.