Therapeutic contact lenses were developed from bacterial cellulose (BC) by the Institute of Chemistry at Brazil’s São Paulo State University (UNESP). In a previous study, cyclodextrins (CD) and medications such as ciprofloxacin (CP) and diclofenac sodium (DS) were incorporated into the lenses to provide therapeutic properties and control drug release. However, significant opacity was seen in the material inherent to cellulose. In order to achieve full material transparency, the lenses were coated with an organic-inorganic hybrid compound containing aluminum alkoxide and glycidoxypropyltrimethoxysilane (GPTS)(H), or chitosan (Q) nanoparticles. This study evaluated the toxicity of these contact lenses to ensure the safety of these materials for future availability to the medical device industry. Lenses composed of BC and coated with either GPTS (H) or chitosan (Q), incorporating ciclodextrin (CD) to release diclofenac sodium (DS) or ciprofloxacin (CP), were submitted to cytotoxicity assays (XTT and Clonogenic Survival), genotoxicity (Comet Assay) and mutagenicity (Cytokinesis-blocked micronucleus assay) directly in cell culture. Statistical analyses were performed using the Tukey and Dunnett or Kruskal-Wallis and Dunn tests. All of the nanoparticles used in the lense coatings did not show cytotoxic effects by the XTT test (p > 0.05; Dunnett). Only materials associated with diclofenac sodium (BC-H-CD-DS and BC-Q-CD-DS) presented significantly different survival fractions compared to negative control (p < 0.001; Dunnett). Genotoxicity evaluation revealed a genotoxic effect in BC-H-CD-DS (p < 0.05; Dunn). All tested lenses did not present any mutagenic effect. These results indicate that improvements in DS incorporation are needed to eliminate toxicity. We demonstrated promising results in the safety of employing BC lenses functionalized with a drug delivery system permitting the bioavailability of ophthalmic drugs. Further studies utilizing other specific tests, such as corneal lineage are required before safe and efficient ophthalmologic use.