We study the response of GaAs photonic crystal membrane resonators to thin film deposition. Slow spectral shifts of the cavity mode of several nanometers are observed at low temperatures, caused by cryo-gettering of background molecules. Heating the membrane resets the drift and shielding will prevent drift altogether. In order to explore the drift as a tool to detect surface layers, or to intentionally shift the cavity resonance frequency, we studied the effect of self-assembled monolayers of polypeptide molecules attached to the membranes. The 2 nm thick monolayers lead to a discrete step in the resonance frequency and partially passivate the surface.Photonic crystal membrane microcavities (PCM) are promising candidates for applications ranging from quantum and classical communication [1], to microlasers [2,3] and sensing devices [4,5]. Due to their ultra small mode volumes [6] and large surface to volume ratio, the PCM resonant frequency is highly sensitive to its environment. While this sensitivity may be exploited for novel sensing applications, it complicates solid-state cavity quantum electrodynamic (QED) experiments that depend on a precise resonance condition between a cavity mode and an embedded single quantum dot (QD) [7,8,9, 10], single atom [11] or single impurity [12]. This paper describes a slow red-shift of the PCM mode emission frequency that can occur at low operation temperatures. We ascribe this shift to molecular condensation on the PCM surface. We further describe methods used to fully curtail the drift, and in addition, we report on the first demonstration of a controlled red-shift of the PCM mode by the adsorption of a self-assembled monolayer (SAM) of polypeptide molecules.We are particularly interested in PCM devices operated at low temperatures in such a way that embedded QDs display a discrete energy spectrum. As a model system a square-lattice PCM geometry with one missing air hole (S1) has been chosen, which is known to confine the fundamental mode in the proximity of the air-semiconductor interface [13]. A single layer of selfassembled InAs QDs was embedded in the 180 nm thick GaAs membrane and emits around 950 nm [14] under non-resonant laser excitation at 780 nm. Figure 1a shows a spectrum of the fundamental cavity mode taken at pump powers of 15 µW, which has been recorded with a micro photoluminescence (micro-PL) setup [15]. At these excitation conditions the cavity mode is clearly visible at 1.3293 eV with a quality factor (Q-factor) of 1900. The 2 µm diameter laser excitation spot has to be positioned with an accuracy of ±0.5 µm with respect to the cavity defect region (Fig. 1c), demonstrating the strongly localized character of the mode. Individual QD transitions are visible under low pump power excitation of 50 nW, which have been identified by their pronounced antibunching signature (not shown). Another set of two spectra was taken 200 min later as shown in Fig. 1b. While the single QD emission energy at 1.31780 ± 2 · 10 −5 eV did not change in the entire observation perio...