Background/Objectives: The design of alternative antipathogenic sprays has recently attracted much attention due to the limitations of existing formulations, such as toxicity and low and narrow efficacy. Polyethyleneimine (PEI) is a great antimicrobial polymer against a wide range of pathogens, but toxicity limits its use. Here, betainized PEI (B-PEI) was synthesized to decrease the toxicity of PEI and protonated with citric acid (CA), boric acid (BA), and HCl to improve antimicrobial activity. Methods: Cytotoxicity of the PEI-based solutions was determined on L929 fibroblast cells. Antibacterial/fungal activity of PEI-based antipathogenic sprays was investigated by microtiter and disc diffusion assays, in addition to bacterial viability and adhesion % of common bacteria and fungi on the PEI-treated masks. Furthermore, the antiviral effect of the PEI-based solutions was determined against SARS-CoV-2 virus. Results: The biosafe concentration of PEI was determined as 1 μg/mL with 75 ± 11% cell viability, but B-PEI and its protonated forms had great biocompatibility even at 1000 μg/mL with more than 85% viability. The antibacterial/fungal effect of non-toxic B-PEI was improved by protonation with BA and HCl with 2.5–10 mg/mL minimum bactericidal/fungicidal concentrations (MBCs/MFCs). Bacterial/fungal viability and adhesion on the mask was almost eliminated by using 50 μL with 5–10 mg/mL of B-PEI-BA. Both protonated bare and betainized PEI show potent antiviral activity against SARS-CoV-2 virus. Conclusions: The toxicity of PEI was overcome by using betainized forms of PEI (B-PEI). Furthermore, the antimicrobial and antiviral efficacy of PEI and B-PEI was improved by protonation with CA, BA, and HCl of amine groups on B-PEI. B-PEI-BA spray solution has great potential as an antipathogenic spray with broad-spectrum antimicrobial potency against harmful bacteria, fungi, and viruses without any toxicity.