Protein hydrolysates and bioactive peptides from various protein sources have demonstrated their effectiveness for the prevention of illness and the improvement of symptoms from several diseases. In particular, the use of microalgae to generate bioactive peptides has received a growing interest because of their potential to be cultivated on non-arable land and high nutritional value. However, scant research is available on the toxicity of peptide-based preparations. The present study aims to evaluate the toxicity of microalgal protein hydrolysates (MPH) from one marine species of microalgae (Bellerochea malleus) to determine the feasibility of their use for functional food applications. Results showed that the oral administration of MPH at three doses (D1, 100 mg kg−1 BW; D2, 400 mg kg−1 BW; and D3, 2000 mg kg−1 BW) to male Wistar rats did not induce any adverse effects or mortality up to13 days of treatment. Data analysis of relative organ weights and biochemical and hematological parameters did not show any significant differences between control and treated groups at the three doses investigated. Data from histopathological observations did not reveal any signs of major toxicity at the doses D1 and D2. However, mild signs of inflammation and necrosis were observed in the kidney of rats fed MPH at D3. All together, these results reveal the overall safety of MPH and provide new evidence for advocating their use for functional food or nutraceutical applications.