One has to keep apart different layers: a) abiogenesis (the emergence of life) vs. evolution (the development of existing life over generations) and b) the incompatibility of biblical accounts of the origin of species with evolution vs. the incompatibility of the belief in God being the creator of life with evolution.
I will first answer the title question and then address the second layer.
Darwin on the origin of life
Charles Darwin himself did never explicitly write that it is the case that life developed gradually by natural processes, but this was due to the impossibility to scientifically prove this possibility at the time. It was his personal conviction, though: he did not believe in teleological or theological explanations of life.
This point is made and shown as valid in the paper: Peretó, J., Bada, J. L., & Lazcano, A. (2009). Charles Darwin and the Origin of Life. Origins of Life and Evolution of the Biosphere, 39(5), 395–406. http://doi.org/10.1007/s11084-009-9172-7
The abstract reads:
When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that “the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable”. Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was impossible to undertake the experimental study of the emergence of life.
They use letters and notes. One of the last letters is quoted in full towards the end of the paper and reaffirms the point:
He was to maintain the same attitude for many years to come, as shown by the letter mailed on March 28, 1882, near the end of his life, to George Charles Wallich (de Beer 1959). In it Darwin wrote that,
«My dear Sir,
You expressed quite correctly my views where you say that I had intentionally left the question of the Origin of Life uncanvassed as being altogether ultra vires in the present state of our knowledge, & that I dealt only with the manner of succession. I have met with no evidence that seems in the least trustworthy, in favour of the so-called Spontaneous generation. I believe that I have somewhere said (but cannot find the passage) that the principle of continuity renders it probable that the principle of life will hereafter be shown to be a part, or consequence of some general law; but this is only conjecture and not science. I know nothing about the Protista, and shall be very glad to read your Lecture when it is published, if you will be so kind as to send me a copy.
I remain, my dear Sir,
Yours very faithfully
Thus, Darwin was convinced, but not able to scientifically demonstrate, that life emerged following laws of nature, i.e. "naturally". Consequently, he withheld this conviction in his scientific publications. As such, Darwin was a true scientist.
God as the creator of life vs. evolution
Darwin himself seemed to be against the idea that God did create life. At least, he saw no conclusive reason to think that he did. The authors of the paper referred to earlier write:
In a letter he sent in February 28, 1882 to D. Mackintosh (Letter 13711, Cambridge University Library, DAR.146:335), he included an indirect reference to Wöhler’s synthesis of urea and added that
«[...] If it is ever found that life can originate on this world, the vital phenomena will come under some general law of nature. Whether the existence of a conscious God can be proved from the existence of the so called laws of nature (i. e. fixed sequence of events) is a perplexing subject, on which I have often thought, but cannot see my way clearly...».
But this does not mean that belief in God is incompatible with evolutionary theory in principle, although standing at odds with the descriptions given in the Bible. As written in Stewart-Williams, S. (2010). Darwin, God and the Meaning of Life: How Evolutionary Theory Undermines Everything You Thought You Knew. Cambridge: Cambridge University Press (a recommended read for all those interested in this problem):
From the moment Darwin put forward his theory, it was obvious to his
contemporaries that, if he was right, the biblical account of the origin
of life must be wrong. In principle, people might have concluded that
the Bible was wrong about the details of how God created life, but not
about the fact that God existed in the ﬁrst place. (p.44)