Self-assembled nanoaggregates of π-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups that make them attractive candidates for the fabrication of bioelectronic materials. We present a computational and theoretical study to resolve the microscopic effects of pH and flow on the non-equilibrium morphology and kinetics of early-stage assembly of an experimentally-realizable optoelectronic peptide that displays pH triggerable assembly. Employing coarse-grained molecular dynamics simulations, we probe the effects of pH on growth kinetics and aggregate morphology to show that control of the peptide protonation state by pH can be used to modulate the assembly rates, degree of molecular alignment, and resulting morphologies within the self-assembling nanoaggregates. We also quantify the time and length scales at which convective flows employed in directed assembly compete with microscopic diffusion to show that flow influences cluster alignment and assembly rate during early-stage assembly only at extremely high shear rates. This suggests that observed improvements in optoelectronic properties at experimentally-accessible shear rates are due to the alignment of large aggregates of hundreds of monomers on time scales in excess of hundreds of nanoseconds. Our work provides new fundamental understanding of the effects of pH and flow to control the morphology and kinetics of early-stage assembly of π-conjugated peptides and lays the groundwork for the rational manipulation of environmental conditions to direct assembly and the attendant emergent optoelectronic properties.