The targeted delivery of enzyme-responsive nanoparticles to specific tissues can be a valuable, minimally invasive approach for imaging or drug delivery applications. In this study, we show for the first time enzyme-directed assembly of intravenously (IV) delivered nanoparticles in ischemic skeletal muscle, which has applications for drug delivery to damaged muscle of the type prevalent in peripheral artery disease (PAD). Specifically, micellar nanoparticles are cleavable by matrix metalloproteinases (MMPs), causing them to undergo a morphological switch and thus aggregate in tissues where these enzymes are upregulated, like ischemic muscle. Here, we demonstrated noninvasive in vivo imaging of these IV-injected nanoparticles through near-infrared dye labeling and in vivo imaging (IVIS) particle tracking in a rat hindlimb ischemia model. Polymer peptide amphiphilic nanoparticles were synthesized and optimized for both MMP cleavage efficiency and near-IR fluorescence. Nanoparticles were injected 4 days after unilateral hindlimb ischemia and were monitored over 28 days using IVIS imaging. Nanoparticles targeted to ischemic muscle over healthy muscle, and ex vivo biodistribution analysis at 7 and 28 days post-injection confirmed targeting to the ischemic muscle as well as off target accumulation in the liver and spleen. Ex vivo histology confirmed particle localization in ischemic but not healthy muscle. Altering the surface charge of the nanoparticles through addition of zwitterionic dye species resulted in improved targeting to the ischemic muscle. To our knowledge, this is the first study to demonstrate the targeted delivery and long term retention of nanoparticles using an enzyme-directed morphology switch. This has implications for noninvasive drug delivery vehicles for treating ischemic muscle, as no minimally invasive, non-surgical options currently exist.