Abstract Transcranial alternating current stimulation (tACS) represents a promising non-invasive treatment for an increasingly wide range of neurological and neuropsychiatric disorders. The ability to use periodically oscillating electric fields to non-invasively engage neural dynamics opens up the possibility of recruiting synaptic plasticity and to modulate brain function. However, despite consistent reports about tACS clinical effectiveness, strong state-dependence combined with the ubiquitous heterogeneity of cortical networks collectively results in high outcome variability. Introducing variations in intrinsic neuronal timescales, we explored how such heterogeneity influences stimulation-induced change in synaptic connectivity. We examined how spike timing dependent plasticity, at the level of cells, intra- and inter-laminar cortical networks, can be selectively and preferentially engaged by periodic stimulation. Using computational simulations informed by human experimental data, we analyzed cortical circuits comprised of multiple cell-types, alongside superficial multi-layered networks expressing distinct layer-specific timescales. Our results show that mismatch in neuronal timescales within and/or between cells - and the resulting variability in excitability, temporal integration properties and frequency tuning - enables selective and directional control on synaptic connectivity by tACS. Our work provides new vistas on how to recruit neural heterogeneity to guide brain plasticity using non-invasive stimulation paradigms. Author summary Brain stimulation techniques, such as transcranial alternating current stimulation (tACS), are increasingly used to treat mental health disorders and to probe brain function. Despite promising results, it remains unclear how these non-invasive interventions impact both the dynamics and connectivity of neural circuits. We developed an interdisciplinary framework showing that heterogeneity in neuronal timescales, and its consequences on cellular excitability and temporal integration properties of cortical neurons, may lead to selective and directional control on synaptic modifications by tACS. Differences in neuron responses resulting from timescale mismatch establishes phase- and frequency-specific tuning relationships which may be recruited by periodic stimuli to guide synaptic plasticity. We confirmed this using both intra - and inter-laminar cortical circuit models comprised of multiple cell-types and informed by experimental data. Our work showcases how heterogeneity might be used to guide synaptic plasticity using non-invasive stimulation paradigms.