With the recently increased interest in probabilistic models, the efficiency of an underlying sampler becomes a crucial consideration. A Hamiltonian Monte Carlo (HMC) sampler is one popular option for models of this kind. Performance of HMC, however, strongly relies on a choice of parameters associated with an integration method for Hamiltonian equations, which up to date remains mainly heuristic or introduce time complexity. We propose a novel computationally inexpensive and flexible approach (we call it Adaptive Tuning or ATune) that, by analyzing the data generated during a burning stage of an HMC simulation, detects a system specific splitting integrator with a set of reliable HMC hyperparameters, including their credible randomization intervals, to be readily used in a production simulation. The method automatically eliminates those values of simulation parameters which could cause undesired extreme scenarios, such as resonance artifacts, low accuracy or poor sampling. The new approach is implemented in the in-house software package \textsf{HaiCS}, with no computational overheads introduced in a production simulation, and can be easily incorporated in any package for Bayesian inference with HMC. The tests on popular statistical models using original HMC and generalized Hamiltonian Monte Carlo (GHMC) reveal the superiority of adaptively tuned methods in terms of stability, performance and accuracy over conventional HMC tuned heuristically and coupled with the well-established integrators. We also claim that the generalized formulation of HMC, i.e. GHMC, is preferable for achieving high sampling performance. The efficiency of the new methodology is assessed in comparison with state-of-the-art samplers, e.g. the No-U-Turn-Sampler (NUTS), in real-world applications, such as endocrine therapy resistance in cancer, modeling of cell-cell adhesion dynamics and influenza epidemic outbreak.