Isolated stellar-mass black holes traversing dense regions of the interstellar medium, such as molecular clouds, are expected to accrete ambient gas. This accretion process can ionize surrounding gas, carving out a low-density ionized cavity within the cloud. The accreting black holes may also possess accretion discs and jets, producing cosmic rays and triggering hadronic and leptonic interactions. In this work, we show that the number of black holes residing in molecular clouds is proportional to the size of the cloud and we estimate the specific black-hole number density to be $\sim 1.2 \times 10 ^{-5}$ per solar mass of cloud, i.e., at least 10 black holes in massive molecular clouds with mass $8.4 \times 10^5$ solar mass. We then estimate the accretion process by Bondi–Hoyle–Lyttleton accretion and the effects brought about on the cloud structures, such as the formation of ionization cavities, and on the production of energetic particles. We show that the accretion rate log($\dot{M}$) [g/s] can reach up to 18 and the ionization cavity can reach up to 1 pc, occupying a substantial region of smaller molecular clouds. We discuss the consequences of the presence of ionization cavities in molecular clouds of different sizes, hence the implications for (i) cloud fragmentation and star formation and (ii) the inhomogeneity in the cloud environment for cosmic-ray transport in molecular clouds.