Doubly-stochastic point processes model the occurrence of events over a spatial domain as an inhomogeneous Poisson process conditioned on the realization of a random intensity function. They are flexible tools for capturing spatial heterogeneity and dependence. However, implementations of doubly-stochastic spatial models are computationally demanding, often have limited theoretical guarantee, and/or rely on restrictive assumptions. We propose a penalized regression method for estimating covariate effects in doubly-stochastic point processes that is computationally efficient and does not require a parametric form or stationarity of the underlying intensity. We establish the consistency and asymptotic normality of the proposed estimator, and develop a covariance estimator that leads to a conservative statistical inference procedure. A simulation study shows the validity of our approach under less restrictive assumptions on the data generating mechanism, and an application to Seattle crime data demonstrates better prediction accuracy compared with existing alternatives.