Advancing quantum technologies depends on the precise control of individual quantum systems, the so-called qubits, and the exploitation of their quantum properties. Nowadays, expanding the number of qubits to be entangled is at the core of the developments of quantum sensors, quantum communications, and even quantum computers. Gaining the ability for selective manipulation of individual qubits within large ensembles is essential for the advancements. The nitrogen-vacancy (NV) center in diamond, known for its spin-dependent fluorescence and facile formation in large quantity, emerges as a prominent candidate for scalable quantum platforms. However, conventional optical and microwave methods for controlling them fall short in spatial selectivity. In this thesis, we proposed and assessed control techniques utilizing the electron beam of a standard scanning electron microscope (SEM) alongside standard methods, leveraging the electron's small de Broglie wavelength for an enhanced resolution. We first developed a homemade confocal microscope tailored for standard techniques of optically detected magnetic resonance (ODMR) specific to NV centers. Additionally, we customized an open-source code to automate and synchronize the instruments. The versatility of our setup allows for a broad range of applications, from the characterization of the samples to conducting quantum sensing experiments. Specifically, we utilized this setup to detect and observe the behavior of free radicals within cells, employing all-optical and microwave T1 relaxometry measurements on fluorescent nanodiamonds ingested by living cells. To perform electron beam-based controls on the NV centers, we interfaced our confocal microscope with a scanning electron microscope (SEM) and developed the modulation of the electron beam in synchrony with the optical and microwave excitations. The idea is to alter the local environment of the target qubit using the magnetic field produced by passing electrons. However, the successful revealing of the selective spin-flip depends on controlling the interaction volume of the electron, extending the NV center coherence, and, increasing the read-out spatial selectivity, so far limited by optical diffraction. While the interaction of the electron beam with the NV centers induces a charge conversion from negatively charged, exhibiting ODMR, to neutral, we leverage this effect to improve the readout spatial resolution. This enhancement is achieved by scanning the electron beam over specific areas to locally convert the NV centers to their neutral state to mute them by filtering out their luminescence. Overall, this thesis presents and assesses original methods for electron-beam-based controls of NV centers' spin and charge state, with a spatial resolution that ultimately could be limited by the electron beam. This illustrates a potential route for the development of versatile solutions for selectively driving spin qubits within ensembles.