The present invention provides for methods of administering by a pulmonary route an effective amount of a bisphosphonate active agent to a subject. Aspects of the invention including administering the active agent to the subject in conjunction with one or more mucosal membrane protecting agents, where the protecting agent may include one or more of a protecting enzyme and/or a protecting amino acid and/or a protecting peptide. Also provided are inhalant compositions for use in practicing methods according to embodiments of the invention. Methods and compositions according to embodiments of the invention find use in a variety of different applications, including but not limited to, the treatment of bone adsorption disease conditions.